rs1372685

Positions:

• chr1-166581264-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 0.572 in 151,814 control chromosomes in the GnomAD database, including 24,943 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 0.57 (24943 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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 = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86786 AN: 151696 Hom.: 24942 Cov.: 31

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.572 AC: 86832 AN: 151814 Hom.: 24943 Cov.: 31 AF XY: 0.568 AC XY: 42119 AN XY: 74184

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.606

Alfa AF: 0.564 Hom.: 9628

Bravo AF: 0.572

Asia WGS AF: 0.482 AC: 1672 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
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: rs1372685; hg19: chr1-166550501;