rs17157992

Variant names:

• chr7-83720391-C-T
• rs17157992
• ENST00000782001.1:n.95-6663C>T

Variant summary

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

The ENST00000782001.1(ENSG00000301806):​n.95-6663C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,962 control chromosomes in the GnomAD database, including 4,815 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 0.15 (4815 hom., cov: 31)
• Consequence: ENSG00000301806 ENST00000782001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 1 publications found

Genes affected

ENSG00000301806 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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
ENSG00000301806	ENST00000782001.1	n.95-6663C>T		intron_variant	Intron 2 of 6
ENSG00000301806	ENST00000782002.1	n.143-6663C>T		intron_variant	Intron 3 of 7
ENSG00000301806	ENST00000782003.1	n.95-9176C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22729 AN: 151844 Hom.: 4794 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0266

Gnomad FIN AF: 0.00595

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0234

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.150 AC: 22793 AN: 151962 Hom.: 4815 Cov.: 31 AF XY: 0.144 AC XY: 10698 AN XY: 74288

African (AFR) AF: 0.472 AC: 19526 AN: 41348

American (AMR) AF: 0.0769 AC: 1174 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3470

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5160

South Asian (SAS) AF: 0.0264 AC: 127 AN: 4816

European-Finnish (FIN) AF: 0.00595 AC: 63 AN: 10586

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0234 AC: 1591 AN: 67992

Other (OTH) AF: 0.113 AC: 238 AN: 2110

Alfa AF: 0.115 Hom.: 3214

Bravo AF: 0.170

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.037
DANN	Benign	0.55
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs17157992; hg19: chr7-83349707;