2-185160008-C-T

Variant names:

• chr2-185160008-C-T
• rs11678036

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 0.557 in 151,814 control chromosomes in the GnomAD database, including 24,398 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 0.56 (24398 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 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: 0.557 AC: 84435 AN: 151696 Hom.: 24374 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.557 AC: 84499 AN: 151814 Hom.: 24398 Cov.: 31 AF XY: 0.559 AC XY: 41501 AN XY: 74208

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.541

Alfa AF: 0.573 Hom.: 4430

Bravo AF: 0.538

Asia WGS AF: 0.639 AC: 2221 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.87
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11678036; hg19: chr2-186024735;