rs1974657

Variant names:

• chr5-148922082-A-G
• rs1974657

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 0.343 in 151,916 control chromosomes in the GnomAD database, including 11,773 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 (11773 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52045 AN: 151798 Hom.: 11743 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.343 AC: 52129 AN: 151916 Hom.: 11773 Cov.: 32 AF XY: 0.336 AC XY: 24966 AN XY: 74268

African (AFR) AF: 0.651 AC: 26925 AN: 41382

American (AMR) AF: 0.239 AC: 3650 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 709 AN: 3466

East Asian (EAS) AF: 0.258 AC: 1330 AN: 5146

South Asian (SAS) AF: 0.285 AC: 1368 AN: 4804

European-Finnish (FIN) AF: 0.175 AC: 1849 AN: 10566

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15335 AN: 67948

Other (OTH) AF: 0.309 AC: 653 AN: 2112

Alfa AF: 0.312 Hom.: 1226

Bravo AF: 0.361

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.55
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1974657; hg19: chr5-148301645;