rs1974657

Variant names:

• chr5-148922082-A-G
• rs1974657

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 151,916 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 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

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.309

Alfa AF: 0.299 Hom.: 1074

Bravo AF: 0.361

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1974657; hg19: chr5-148301645;