rs973406

Variant names:

• chr2-176245003-C-A
• rs973406

Your query was ambiguous. Multiple possible variants found:

• chr2-176245003-C-A
• chr2-176245003-C-G
• chr2-176245003-C-T

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 0.198 in 152,038 control chromosomes in the GnomAD database, including 3,673 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 0.20 (3673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.262 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: 0.199 AC: 30163 AN: 151920 Hom.: 3669 Cov.: 32

Gnomad AFR AF: 0.0542

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.198 AC: 30179 AN: 152038 Hom.: 3673 Cov.: 32 AF XY: 0.197 AC XY: 14644 AN XY: 74316

African (AFR) AF: 0.0542 AC: 2248 AN: 41496

American (AMR) AF: 0.231 AC: 3534 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3470

East Asian (EAS) AF: 0.180 AC: 930 AN: 5168

South Asian (SAS) AF: 0.0970 AC: 467 AN: 4812

European-Finnish (FIN) AF: 0.316 AC: 3332 AN: 10552

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17997 AN: 67954

Other (OTH) AF: 0.202 AC: 425 AN: 2108

Alfa AF: 0.212 Hom.: 3323

Bravo AF: 0.193

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs973406; hg19: chr2-177109731;