chr1-196797447-T-C

Variant names:

• chr1-196797447-T-C
• rs644598

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 0.262 in 131,812 control chromosomes in the GnomAD database, including 9,273 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 0.26 (9273 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 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: 0.262 AC: 34500 AN: 131682 Hom.: 9258 Cov.: 22

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.262 AC: 34533 AN: 131812 Hom.: 9273 Cov.: 22 AF XY: 0.258 AC XY: 16543 AN XY: 64044

African (AFR) AF: 0.400 AC: 12049 AN: 30126

American (AMR) AF: 0.289 AC: 3964 AN: 13700

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 590 AN: 3124

East Asian (EAS) AF: 0.496 AC: 2455 AN: 4948

South Asian (SAS) AF: 0.192 AC: 734 AN: 3814

European-Finnish (FIN) AF: 0.133 AC: 1308 AN: 9822

Middle Eastern (MID) AF: 0.272 AC: 68 AN: 250

European-Non Finnish (NFE) AF: 0.200 AC: 12691 AN: 63380

Other (OTH) AF: 0.241 AC: 427 AN: 1774

Alfa AF: 0.241 Hom.: 991

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs644598; hg19: chr1-196766577;