chr2-175919410-T-C

Variant names:

• chr2-175919410-T-C
• rs1020410

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 0.345 in 152,066 control chromosomes in the GnomAD database, including 9,579 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 0.34 (9579 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 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: 0.345 AC: 52397 AN: 151948 Hom.: 9579 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.345 AC: 52426 AN: 152066 Hom.: 9579 Cov.: 32 AF XY: 0.347 AC XY: 25788 AN XY: 74348

African (AFR) AF: 0.440 AC: 18262 AN: 41480

American (AMR) AF: 0.287 AC: 4380 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1091 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1508 AN: 5162

South Asian (SAS) AF: 0.589 AC: 2836 AN: 4814

European-Finnish (FIN) AF: 0.246 AC: 2598 AN: 10582

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20673 AN: 67962

Other (OTH) AF: 0.321 AC: 677 AN: 2106

Alfa AF: 0.324 Hom.: 16516

Bravo AF: 0.345

Asia WGS AF: 0.397 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.2
DANN	Benign	0.62
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs1020410; hg19: chr2-176784138;