rs2365269

Positions:

• chr1-61594541-A-G
• chr1-61594541-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 0.744 in 152,030 control chromosomes in the GnomAD database, including 42,337 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 0.74 (42337 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

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 = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112957 AN: 151912 Hom.: 42297 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.744 AC: 113052 AN: 152030 Hom.: 42337 Cov.: 31 AF XY: 0.748 AC XY: 55565 AN XY: 74320

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.761

Alfa AF: 0.694 Hom.: 32216

Bravo AF: 0.743

Asia WGS AF: 0.719 AC: 2500 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	0.26
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2365269; hg19: chr1-62060213;