rs2341263

Positions:

• chr1-73617352-C-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 0.276 in 151,980 control chromosomes in the GnomAD database, including 5,912 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 0.28 (5912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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: 0.276 AC: 41890 AN: 151862 Hom.: 5903 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.276 AC: 41931 AN: 151980 Hom.: 5912 Cov.: 32 AF XY: 0.281 AC XY: 20849 AN XY: 74300

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.262

Alfa AF: 0.262 Hom.: 8978

Bravo AF: 0.273

Asia WGS AF: 0.182 AC: 635 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	3.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2341263; hg19: chr1-74083035;