1-70500770-T-C

Position:

• chr1-70500770-T-C

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 0.434 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.449

Alfa AF: 0.502 Hom.: 25393

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

Splicing

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

Publications

LitVar

Other links and lift over

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