1-196612252-C-T

Variant names:

• chr1-196612252-C-T
• rs4507960

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 0.894 in 152,240 control chromosomes in the GnomAD database, including 62,618 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 0.89 (62618 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 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: 0.894 AC: 136047 AN: 152122 Hom.: 62603 Cov.: 33

Gnomad AFR AF: 0.651

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.894 AC: 136108 AN: 152240 Hom.: 62618 Cov.: 33 AF XY: 0.896 AC XY: 66694 AN XY: 74442

African (AFR) AF: 0.651 AC: 27016 AN: 41496

American (AMR) AF: 0.962 AC: 14714 AN: 15300

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3471 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4898 AN: 5158

South Asian (SAS) AF: 0.927 AC: 4478 AN: 4830

European-Finnish (FIN) AF: 0.998 AC: 10599 AN: 10624

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67789 AN: 68042

Other (OTH) AF: 0.919 AC: 1940 AN: 2112

Alfa AF: 0.934 Hom.: 8414

Bravo AF: 0.882

Asia WGS AF: 0.909 AC: 3162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.83
DANN	Benign	0.75
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs4507960; hg19: chr1-196581382;