rs62057608

Variant names:

• chr16-35447822-C-T
• rs62057608
• ENST00000562068.2:n.325G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000568619.3(ENSG00000293007):​n.591G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0266 in 454,902 control chromosomes in the GnomAD database, including 242 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.026 (64 hom., cov: 34)
  • Exomes 𝑓: 0.027 (178 hom.)
• Consequence: ENSG00000293007 ENST00000568619.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47
• Publications: 3 publications found

Genes affected

ZNF971P (HGNC:51848): (zinc finger protein 971, pseudogene)

ENSG00000293007 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0259 (3939/152246) while in subpopulation NFE AF = 0.0401 (2724/68000). AF 95% confidence interval is 0.0388. There are 64 homozygotes in GnomAd4. There are 1863 alleles in the male GnomAd4 subpopulation. Median coverage is 34. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 64 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568619.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF971P	ENST00000562068.2	TSL:6	n.325G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000293007	ENST00000568619.3	TSL:3	n.591G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000293007	ENST00000720087.1		n.357G>A		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0259 AC: 3939 AN: 152128 Hom.: 64 Cov.: 34

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0160

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0234

GnomAD2 exomes AF: 0.0216 AC: 2981 AN: 138018 AF XY: 0.0207

Gnomad AFR exome AF: 0.0106

Gnomad AMR exome AF: 0.0111

Gnomad ASJ exome AF: 0.0141

Gnomad EAS exome AF: 0.0000954

Gnomad FIN exome AF: 0.0370

Gnomad NFE exome AF: 0.0383

Gnomad OTH exome AF: 0.0253

GnomAD4 exome AF: 0.0269 AC: 8141 AN: 302656 Hom.: 178 Cov.: 0 AF XY: 0.0248 AC XY: 4273 AN XY: 172262

African (AFR) AF: 0.0115 AC: 99 AN: 8590

American (AMR) AF: 0.0114 AC: 309 AN: 27138

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 146 AN: 10730

East Asian (EAS) AF: 0.00 AC: 0 AN: 9152

South Asian (SAS) AF: 0.00304 AC: 181 AN: 59448

European-Finnish (FIN) AF: 0.0396 AC: 510 AN: 12868

Middle Eastern (MID) AF: 0.00359 AC: 10 AN: 2782

European-Non Finnish (NFE) AF: 0.0412 AC: 6500 AN: 157672

Other (OTH) AF: 0.0270 AC: 386 AN: 14276

GnomAD4 genome AF: 0.0259 AC: 3939 AN: 152246 Hom.: 64 Cov.: 34 AF XY: 0.0250 AC XY: 1863 AN XY: 74442

African (AFR) AF: 0.0108 AC: 448 AN: 41570

American (AMR) AF: 0.0160 AC: 245 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.00331 AC: 16 AN: 4828

European-Finnish (FIN) AF: 0.0363 AC: 385 AN: 10596

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0401 AC: 2724 AN: 68000

Other (OTH) AF: 0.0232 AC: 49 AN: 2114

Alfa AF: 0.0251 Hom.: 36

Bravo AF: 0.0238

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.6
DANN	Benign	0.61
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs62057608; hg19: chr16-34682193;