chr1-195407805-C-T

Position:

• chr1-195407805-C-T

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 0.619 in 151,886 control chromosomes in the GnomAD database, including 30,005 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 0.62 (30005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93946 AN: 151768 Hom.: 29974 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.619 AC: 94028 AN: 151886 Hom.: 30005 Cov.: 32 AF XY: 0.615 AC XY: 45671 AN XY: 74212

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.616

Alfa AF: 0.652 Hom.: 5699

Bravo AF: 0.613

Asia WGS AF: 0.464 AC: 1613 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324713; hg19: chr1-195376935; COSMIC: COSV60010621;