chr2-196180353-G-A

Variant names:

• chr2-196180353-G-A
• rs1378624

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 151,944 control chromosomes in the GnomAD database, including 6,158 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 (6158 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 42051 AN: 151826 Hom.: 6151 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.277 AC: 42090 AN: 151944 Hom.: 6158 Cov.: 32 AF XY: 0.276 AC XY: 20473 AN XY: 74258

African (AFR) AF: 0.354 AC: 14681 AN: 41418

American (AMR) AF: 0.302 AC: 4609 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3468

East Asian (EAS) AF: 0.142 AC: 733 AN: 5166

South Asian (SAS) AF: 0.223 AC: 1076 AN: 4818

European-Finnish (FIN) AF: 0.218 AC: 2294 AN: 10530

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.247 AC: 16806 AN: 67952

Other (OTH) AF: 0.278 AC: 587 AN: 2110

Alfa AF: 0.260 Hom.: 14571

Bravo AF: 0.289

Asia WGS AF: 0.194 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.065
DANN	Benign	0.48
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1378624; hg19: chr2-197045077;