rs2841974

Variant names:

• chr1-162989228-G-A
• rs2841974

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 0.343 in 151,700 control chromosomes in the GnomAD database, including 9,074 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 0.34 (9074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 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: 0.343 AC: 51973 AN: 151582 Hom.: 9071 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.343 AC: 51995 AN: 151700 Hom.: 9074 Cov.: 32 AF XY: 0.340 AC XY: 25223 AN XY: 74140

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.351

Alfa AF: 0.328 Hom.: 5118

Bravo AF: 0.337

Asia WGS AF: 0.262 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.066
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2841974; hg19: chr1-162959018;