1-42371864-G-C

Variant names:

• chr1-42371864-G-C
• rs12036838

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 0.352 in 152,034 control chromosomes in the GnomAD database, including 10,926 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 0.35 (10926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.352 AC: 53513 AN: 151914 Hom.: 10922 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.352 AC: 53521 AN: 152034 Hom.: 10926 Cov.: 32 AF XY: 0.348 AC XY: 25877 AN XY: 74302

African (AFR) AF: 0.142 AC: 5878 AN: 41484

American (AMR) AF: 0.417 AC: 6372 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1663 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1546 AN: 5168

South Asian (SAS) AF: 0.256 AC: 1237 AN: 4826

European-Finnish (FIN) AF: 0.462 AC: 4866 AN: 10538

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30754 AN: 67968

Other (OTH) AF: 0.378 AC: 797 AN: 2110

Alfa AF: 0.400 Hom.: 1645

Bravo AF: 0.348

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.69
DANN	Benign	0.70
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs12036838; hg19: chr1-42837535;