rs1938492

Variant names:

• chr1-65652146-A-C
• rs1938492

Your query was ambiguous. Multiple possible variants found:

• chr1-65652146-A-C
• chr1-65652146-A-G
• chr1-65652146-A-T

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 0.437 in 151,752 control chromosomes in the GnomAD database, including 15,236 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 0.44 (15236 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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 (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.437 AC: 66256 AN: 151634 Hom.: 15198 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.437 AC: 66355 AN: 151752 Hom.: 15236 Cov.: 31 AF XY: 0.445 AC XY: 33044 AN XY: 74180

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.423

Alfa AF: 0.404 Hom.: 1597

Bravo AF: 0.436

Asia WGS AF: 0.624 AC: 2168 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	2.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938492; hg19: chr1-66117829; COSMIC: COSV59170817;