rs1938492

Positions:

• chr1-65652146-A-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;