rs62034322

Variant names:

• chr16-28524513-G-A
• rs62034322
• ENST00000779983.1:n.86+1810C>T

Variant summary

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

The ENST00000779983.1(ENSG00000301581):​n.86+1810C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,672 control chromosomes in the GnomAD database, including 8,731 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 0.32 (8731 hom., cov: 30)
• Consequence: ENSG00000301581 ENST00000779983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 11 publications found

Genes affected

ENSG00000301581 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 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
ENSG00000301581	ENST00000779983.1	n.86+1810C>T		intron_variant	Intron 1 of 2
ENSG00000301581	ENST00000779984.1	n.58+1810C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48909 AN: 151554 Hom.: 8719 Cov.: 30

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.0814

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.293

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.323 AC: 48963 AN: 151672 Hom.: 8731 Cov.: 30 AF XY: 0.322 AC XY: 23863 AN XY: 74098

African (AFR) AF: 0.237 AC: 9813 AN: 41386

American (AMR) AF: 0.339 AC: 5168 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 982 AN: 3462

East Asian (EAS) AF: 0.0816 AC: 417 AN: 5110

South Asian (SAS) AF: 0.196 AC: 941 AN: 4796

European-Finnish (FIN) AF: 0.474 AC: 4978 AN: 10506

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25828 AN: 67862

Other (OTH) AF: 0.294 AC: 619 AN: 2106

Alfa AF: 0.366 Hom.: 1431

Bravo AF: 0.312

Asia WGS AF: 0.202 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.28
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs62034322; hg19: chr16-28535834;