17-78961249-T-C

Variant names:

• chr17-78961249-T-C
• rs8074370

Variant summary

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

The variant allele was found at a frequency of 0.642 in 152,062 control chromosomes in the GnomAD database, including 36,292 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 0.64 (36292 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 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

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97614 AN: 151944 Hom.: 36298 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.642 AC: 97603 AN: 152062 Hom.: 36292 Cov.: 32 AF XY: 0.636 AC XY: 47283 AN XY: 74330

African (AFR) AF: 0.293 AC: 12151 AN: 41456

American (AMR) AF: 0.604 AC: 9226 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2754 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1233 AN: 5166

South Asian (SAS) AF: 0.569 AC: 2736 AN: 4810

European-Finnish (FIN) AF: 0.834 AC: 8848 AN: 10606

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.858 AC: 58342 AN: 67978

Other (OTH) AF: 0.660 AC: 1391 AN: 2108

Alfa AF: 0.779 Hom.: 187745

Bravo AF: 0.607

Asia WGS AF: 0.380 AC: 1323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.54
DANN	Benign	0.78
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs8074370; hg19: chr17-76957331;