chr1-96478438-T-C

Variant names:

• chr1-96478438-T-C
• rs1973993

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 0.495 in 152,072 control chromosomes in the GnomAD database, including 21,011 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 0.50 (21011 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 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: 0.496 AC: 75341 AN: 151954 Hom.: 21012 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.495 AC: 75345 AN: 152072 Hom.: 21011 Cov.: 33 AF XY: 0.497 AC XY: 36980 AN XY: 74360

African (AFR) AF: 0.235 AC: 9733 AN: 41490

American (AMR) AF: 0.562 AC: 8586 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1872 AN: 3470

East Asian (EAS) AF: 0.884 AC: 4561 AN: 5162

South Asian (SAS) AF: 0.501 AC: 2414 AN: 4822

European-Finnish (FIN) AF: 0.597 AC: 6304 AN: 10562

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40196 AN: 67980

Other (OTH) AF: 0.500 AC: 1056 AN: 2114

Alfa AF: 0.563 Hom.: 85487

Bravo AF: 0.485

Asia WGS AF: 0.691 AC: 2397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	8.6
DANN	Benign	0.49
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1973993; hg19: chr1-96943994;