chr2-173060323-T-C

Variant names:

• chr2-173060323-T-C
• rs10187560

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 0.614 in 151,912 control chromosomes in the GnomAD database, including 29,371 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 0.61 (29371 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 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: 0.614 AC: 93191 AN: 151792 Hom.: 29376 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.614 AC: 93213 AN: 151912 Hom.: 29371 Cov.: 31 AF XY: 0.605 AC XY: 44894 AN XY: 74232

African (AFR) AF: 0.582 AC: 24128 AN: 41424

American (AMR) AF: 0.453 AC: 6928 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1317 AN: 5168

South Asian (SAS) AF: 0.505 AC: 2429 AN: 4812

European-Finnish (FIN) AF: 0.658 AC: 6930 AN: 10538

Middle Eastern (MID) AF: 0.659 AC: 191 AN: 290

European-Non Finnish (NFE) AF: 0.694 AC: 47139 AN: 67924

Other (OTH) AF: 0.582 AC: 1223 AN: 2100

Alfa AF: 0.659 Hom.: 17973

Bravo AF: 0.596

Asia WGS AF: 0.387 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.61
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10187560; hg19: chr2-173925051;