1-11853700-T-C

Position:

• chr1-11853700-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 0.434 in 151,808 control chromosomes in the GnomAD database, including 15,212 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 0.43 (15212 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.434 AC: 65818 AN: 151690 Hom.: 15194 Cov.: 31

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.434 AC: 65871 AN: 151808 Hom.: 15212 Cov.: 31 AF XY: 0.431 AC XY: 31977 AN XY: 74172

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.420

Alfa AF: 0.397 Hom.: 12850

Bravo AF: 0.431

Asia WGS AF: 0.352 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs198375; hg19: chr1-11913757;