1-65690338-G-T

Variant names:

• chr1-65690338-G-T
• rs2211651

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 0.434 in 151,922 control chromosomes in the GnomAD database, including 14,971 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 0.43 (14971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 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: 0.433 AC: 65806 AN: 151804 Hom.: 14949 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.434 AC: 65884 AN: 151922 Hom.: 14971 Cov.: 32 AF XY: 0.442 AC XY: 32808 AN XY: 74230

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.420

Alfa AF: 0.381 Hom.: 14654

Bravo AF: 0.432

Asia WGS AF: 0.621 AC: 2155 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	0.12
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2211651; hg19: chr1-66156021; COSMIC: COSV59950623;