1-70500770-T-C

Variant names:

• chr1-70500770-T-C
• rs655938

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 0.434 in 152,014 control chromosomes in the GnomAD database, including 15,241 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 0.43 (15241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.826
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 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: 0.434 AC: 65888 AN: 151898 Hom.: 15241 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.434 AC: 65908 AN: 152014 Hom.: 15241 Cov.: 32 AF XY: 0.433 AC XY: 32158 AN XY: 74300

African (AFR) AF: 0.259 AC: 10755 AN: 41466

American (AMR) AF: 0.434 AC: 6633 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1508 AN: 3470

East Asian (EAS) AF: 0.376 AC: 1941 AN: 5168

South Asian (SAS) AF: 0.465 AC: 2235 AN: 4802

European-Finnish (FIN) AF: 0.524 AC: 5535 AN: 10564

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35717 AN: 67952

Other (OTH) AF: 0.449 AC: 947 AN: 2108

Alfa AF: 0.500 Hom.: 30000

Bravo AF: 0.419

Asia WGS AF: 0.412 AC: 1432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.58
DANN	Benign	0.82
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs655938; hg19: chr1-70966453; COSMIC: COSV59954197;