2-41116081-G-C

Variant names:

• chr2-41116081-G-C
• rs2194437

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 0.16 in 151,944 control chromosomes in the GnomAD database, including 4,077 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 0.16 (4077 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.909

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 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: 0.160 AC: 24330 AN: 151826 Hom.: 4059 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0355

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.160 AC: 24383 AN: 151944 Hom.: 4077 Cov.: 32 AF XY: 0.159 AC XY: 11843 AN XY: 74260

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0646

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.0921

Gnomad4 FIN AF: 0.0693

Gnomad4 NFE AF: 0.0355

Gnomad4 OTH AF: 0.155

Alfa AF: 0.0338 Hom.: 72

Bravo AF: 0.179

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.56
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2194437; hg19: chr2-41343221;