2-218195098-T-C

Variant names:

• chr2-218195098-T-C
• rs4674271

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 0.045 in 152,244 control chromosomes in the GnomAD database, including 321 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 0.045 (321 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 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: 0.0451 AC: 6865 AN: 152126 Hom.: 323 Cov.: 33

Gnomad AFR AF: 0.00816

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0967

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0450 AC: 6854 AN: 152244 Hom.: 321 Cov.: 33 AF XY: 0.0474 AC XY: 3529 AN XY: 74432

African (AFR) AF: 0.00813 AC: 338 AN: 41554

American (AMR) AF: 0.113 AC: 1728 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3472

East Asian (EAS) AF: 0.220 AC: 1137 AN: 5178

South Asian (SAS) AF: 0.0960 AC: 463 AN: 4824

European-Finnish (FIN) AF: 0.0251 AC: 266 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0399 AC: 2716 AN: 68006

Other (OTH) AF: 0.0455 AC: 96 AN: 2112

Alfa AF: 0.0402 Hom.: 91

Bravo AF: 0.0517

Asia WGS AF: 0.127 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.75
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4674271; hg19: chr2-219059821;