rs6565051

Variant names:

• chr16-82625123-G-A
• rs6565051
• ENST00000793365.1:n.1013+1174C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-82625123-G-A
• chr16-82625123-G-C
• chr16-82625123-G-T

Variant summary

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

The ENST00000793365.1(ENSG00000303284):​n.1013+1174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,148 control chromosomes in the GnomAD database, including 39,872 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 0.72 (39872 hom., cov: 33)
• Consequence: ENSG00000303284 ENST00000793365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 5 publications found

Genes affected

ENSG00000303284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 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
ENSG00000303284	ENST00000793365.1	n.1013+1174C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109625 AN: 152030 Hom.: 39843 Cov.: 33

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.721 AC: 109694 AN: 152148 Hom.: 39872 Cov.: 33 AF XY: 0.723 AC XY: 53787 AN XY: 74404

African (AFR) AF: 0.672 AC: 27873 AN: 41484

American (AMR) AF: 0.632 AC: 9668 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2305 AN: 3472

East Asian (EAS) AF: 0.654 AC: 3382 AN: 5174

South Asian (SAS) AF: 0.732 AC: 3532 AN: 4824

European-Finnish (FIN) AF: 0.852 AC: 9014 AN: 10586

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51619 AN: 67996

Other (OTH) AF: 0.673 AC: 1421 AN: 2110

Alfa AF: 0.727 Hom.: 33045

Bravo AF: 0.700

Asia WGS AF: 0.653 AC: 2273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6565051; hg19: chr16-82658728;