1-65642834-C-T

Variant names:

• chr1-65642834-C-T
• rs2154384

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 0.438 in 151,974 control chromosomes in the GnomAD database, including 15,289 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 (15289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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: 66408 AN: 151856 Hom.: 15251 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.438 AC: 66507 AN: 151974 Hom.: 15289 Cov.: 32 AF XY: 0.446 AC XY: 33137 AN XY: 74252

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.423

Alfa AF: 0.404 Hom.: 1602

Bravo AF: 0.436

Asia WGS AF: 0.622 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2154384; hg19: chr1-66108517; COSMIC: COSV62746514;