2-191827044-C-T

Variant names:

• chr2-191827044-C-T
• rs4853643

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 0.21 in 151,976 control chromosomes in the GnomAD database, including 3,624 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 0.21 (3624 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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: 0.210 AC: 31888 AN: 151858 Hom.: 3623 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.210 AC: 31914 AN: 151976 Hom.: 3624 Cov.: 32 AF XY: 0.212 AC XY: 15753 AN XY: 74278

African (AFR) AF: 0.232 AC: 9622 AN: 41454

American (AMR) AF: 0.242 AC: 3705 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3464

East Asian (EAS) AF: 0.464 AC: 2399 AN: 5166

South Asian (SAS) AF: 0.240 AC: 1153 AN: 4806

European-Finnish (FIN) AF: 0.166 AC: 1747 AN: 10540

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12002 AN: 67952

Other (OTH) AF: 0.200 AC: 422 AN: 2112

Alfa AF: 0.182 Hom.: 1362

Bravo AF: 0.217

Asia WGS AF: 0.327 AC: 1131 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.99
DANN	Benign	0.39
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs4853643; hg19: chr2-192691770;