rs1765805

chr1-231462108-T-Achr1-231462108-T-Cchr1-231462108-T-G

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 0.697 in 152,074 control chromosomes in the GnomAD database, including 38,499 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 0.70 (38499 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 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: 0.696 AC: 105823 AN: 151956 Hom.: 38433 Cov.: 31

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.697 AC: 105947 AN: 152074 Hom.: 38499 Cov.: 31 AF XY: 0.688 AC XY: 51161 AN XY: 74340

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.670

Alfa AF: 0.659 Hom.: 3987

Bravo AF: 0.719

Asia WGS AF: 0.623 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.056
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1765805; hg19: chr1-231597854;