rs17841343

Variant names:

• chr16-49921211-G-A
• rs17841343
• ENST00000563124.2:n.1607C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000563124.2(ENSG00000261751):​n.1607C>T 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 0.339 in 152,080 control chromosomes in the GnomAD database, including 9,505 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 0.34 (9504 hom., cov: 32)
  • Exomes 𝑓: 0.27 (1 hom.)
• Consequence: ENSG00000261751 ENST00000563124.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 6 publications found

Genes affected

ENSG00000261751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261751	ENST00000563124.2	n.1607C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51460 AN: 151940 Hom.: 9463 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.342

GnomAD4 exome AF: 0.273 AC: 6 AN: 22 Hom.: 1 Cov.: 0 AF XY: 0.333 AC XY: 4 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.214 AC: 3 AN: 14

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.339 AC: 51555 AN: 152058 Hom.: 9504 Cov.: 32 AF XY: 0.341 AC XY: 25328 AN XY: 74314

African (AFR) AF: 0.490 AC: 20316 AN: 41432

American (AMR) AF: 0.281 AC: 4291 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 851 AN: 3466

East Asian (EAS) AF: 0.263 AC: 1358 AN: 5170

South Asian (SAS) AF: 0.451 AC: 2171 AN: 4810

European-Finnish (FIN) AF: 0.317 AC: 3351 AN: 10580

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.267 AC: 18152 AN: 67992

Other (OTH) AF: 0.342 AC: 724 AN: 2114

Alfa AF: 0.293 Hom.: 3349

Bravo AF: 0.339

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs17841343; hg19: chr16-49955122;