chr7-81774578-G-T

Variant names:

• chr7-81774578-G-T
• rs17501108

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.108 in 152,062 control chromosomes in the GnomAD database, including 907 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 0.11 (907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 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: 0.107 AC: 16333 AN: 151944 Hom.: 904 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00964

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.108 AC: 16354 AN: 152062 Hom.: 907 Cov.: 32 AF XY: 0.108 AC XY: 7997 AN XY: 74336

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0772

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.00966

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0858

Alfa AF: 0.112 Hom.: 226

Bravo AF: 0.101

Asia WGS AF: 0.0700 AC: 247 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17501108; hg19: chr7-81403894;