rs6850768

Positions:

• chr4-112797744-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503353.1(ENSG00000250500):​n.658G>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 0.307 in 172,086 control chromosomes in the GnomAD database, including 8,289 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 0.31 (7593 hom., cov: 32)
  • Exomes 𝑓: 0.26 (696 hom.)
• Consequence: ENST00000503353.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANK2	NM_001354269.3	c.72+91527C>T		intron_variant			NP_001341198.1
ANK2	NM_001386148.2	c.72+91527C>T		intron_variant			NP_001373077.1
ANK2	NM_001386186.2	c.72+91527C>T		intron_variant			NP_001373115.1
ANK2	NM_001386187.2	c.72+91527C>T		intron_variant			NP_001373116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000503353.1	n.658G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47512 AN: 151858 Hom.: 7575 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.339

GnomAD4 exome AF: 0.262 AC: 5261 AN: 20110 Hom.: 696 Cov.: 0 AF XY: 0.265 AC XY: 3153 AN XY: 11878

Gnomad4 AFR exome AF: 0.321

Gnomad4 AMR exome AF: 0.260

Gnomad4 ASJ exome AF: 0.272

Gnomad4 EAS exome AF: 0.314

Gnomad4 SAS exome AF: 0.251

Gnomad4 FIN exome AF: 0.302

Gnomad4 NFE exome AF: 0.240

Gnomad4 OTH exome AF: 0.248

GnomAD4 genome AF: 0.313 AC: 47562 AN: 151976 Hom.: 7593 Cov.: 32 AF XY: 0.315 AC XY: 23354 AN XY: 74250

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.343

Alfa AF: 0.295 Hom.: 1608

Bravo AF: 0.316

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	2.5
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6850768; hg19: chr4-113718900;