2-238205599-T-C

Variant names:

• chr2-238205599-T-C
• rs13033116

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 0.277 in 150,098 control chromosomes in the GnomAD database, including 6,116 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 0.28 (6116 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 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: 0.277 AC: 41586 AN: 149994 Hom.: 6111 Cov.: 29

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.277 AC: 41601 AN: 150098 Hom.: 6116 Cov.: 29 AF XY: 0.277 AC XY: 20284 AN XY: 73118

African (AFR) AF: 0.178 AC: 7256 AN: 40668

American (AMR) AF: 0.255 AC: 3845 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3456

East Asian (EAS) AF: 0.211 AC: 1077 AN: 5112

South Asian (SAS) AF: 0.367 AC: 1740 AN: 4742

European-Finnish (FIN) AF: 0.337 AC: 3396 AN: 10072

Middle Eastern (MID) AF: 0.285 AC: 82 AN: 288

European-Non Finnish (NFE) AF: 0.333 AC: 22542 AN: 67668

Other (OTH) AF: 0.272 AC: 570 AN: 2096

Alfa AF: 0.308 Hom.: 954

Bravo AF: 0.266

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.85
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs13033116; hg19: chr2-239114240;