rs6501016

Variant names:

• chr16-7725264-T-A
• rs6501016
• ENST00000777597.1:n.403-31803A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-7725264-T-A
• chr16-7725264-T-C
• chr16-7725264-T-G

Variant summary

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

The ENST00000777597.1(ENSG00000301273):​n.403-31803A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,134 control chromosomes in the GnomAD database, including 50,669 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 0.80 (50669 hom., cov: 32)
• Consequence: ENSG00000301273 ENST00000777597.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 3 publications found

Genes affected

ENSG00000301273 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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
ENSG00000301273	ENST00000777597.1	n.403-31803A>T		intron_variant	Intron 3 of 3
ENSG00000301273	ENST00000777598.1	n.311-31803A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122029 AN: 152016 Hom.: 50661 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.802 AC: 122071 AN: 152134 Hom.: 50669 Cov.: 32 AF XY: 0.806 AC XY: 59898 AN XY: 74348

African (AFR) AF: 0.563 AC: 23373 AN: 41486

American (AMR) AF: 0.901 AC: 13772 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3025 AN: 3470

East Asian (EAS) AF: 0.947 AC: 4893 AN: 5168

South Asian (SAS) AF: 0.923 AC: 4445 AN: 4814

European-Finnish (FIN) AF: 0.838 AC: 8870 AN: 10586

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60808 AN: 68016

Other (OTH) AF: 0.836 AC: 1764 AN: 2110

Alfa AF: 0.833 Hom.: 6701

Bravo AF: 0.798

Asia WGS AF: 0.913 AC: 3171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.44
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs6501016; hg19: chr16-7775266;