chr1-43327136-C-T

Variant names:

• chr1-43327136-C-T
• rs12076751

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.326 in 151,934 control chromosomes in the GnomAD database, including 8,433 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 0.33 (8433 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49457 AN: 151816 Hom.: 8427 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.0984

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.326 AC: 49496 AN: 151934 Hom.: 8433 Cov.: 31 AF XY: 0.321 AC XY: 23855 AN XY: 74278

African (AFR) AF: 0.265 AC: 10982 AN: 41422

American (AMR) AF: 0.375 AC: 5720 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1429 AN: 3458

East Asian (EAS) AF: 0.0983 AC: 509 AN: 5180

South Asian (SAS) AF: 0.149 AC: 719 AN: 4816

European-Finnish (FIN) AF: 0.331 AC: 3493 AN: 10548

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25380 AN: 67944

Other (OTH) AF: 0.374 AC: 789 AN: 2110

Alfa AF: 0.348 Hom.: 2019

Bravo AF: 0.328

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.49
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12076751; hg19: chr1-43792807;