chr1-115012691-T-C

Position:

• chr1-115012691-T-C

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 0.852 in 152,278 control chromosomes in the GnomAD database, including 55,317 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 0.85 (55317 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.852 AC: 129639 AN: 152160 Hom.: 55275 Cov.: 34

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.852 AC: 129738 AN: 152278 Hom.: 55317 Cov.: 34 AF XY: 0.852 AC XY: 63457 AN XY: 74458

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.830

Alfa AF: 0.858 Hom.: 8814

Bravo AF: 0.858

Asia WGS AF: 0.947 AC: 3294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.59
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12740035; hg19: chr1-115555312;