chr7-81777764-T-C

Variant names:

• chr7-81777764-T-C
• rs1558001

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 0.633 in 151,982 control chromosomes in the GnomAD database, including 31,125 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 0.63 (31125 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 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: 0.633 AC: 96190 AN: 151864 Hom.: 31087 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.633 AC: 96272 AN: 151982 Hom.: 31125 Cov.: 32 AF XY: 0.631 AC XY: 46876 AN XY: 74262

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.635

Alfa AF: 0.603 Hom.: 27505

Bravo AF: 0.639

Asia WGS AF: 0.656 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558001; hg19: chr7-81407080;