chr1-196115362-C-T

Variant names:

• chr1-196115362-C-T
• rs6696438

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 0.116 in 152,154 control chromosomes in the GnomAD database, including 1,130 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 0.12 (1130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.926

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.227 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: 0.116 AC: 17595 AN: 152036 Hom.: 1125 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.116 AC: 17617 AN: 152154 Hom.: 1130 Cov.: 32 AF XY: 0.120 AC XY: 8897 AN XY: 74368

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.117

Alfa AF: 0.115 Hom.: 502

Bravo AF: 0.108

Asia WGS AF: 0.228 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6696438; hg19: chr1-196084492;