2-75448734-T-C

Variant names:

• chr2-75448734-T-C
• rs10201616

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 0.225 in 152,102 control chromosomes in the GnomAD database, including 4,237 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 0.23 (4237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 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: 0.225 AC: 34237 AN: 151984 Hom.: 4235 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.225 AC: 34256 AN: 152102 Hom.: 4237 Cov.: 32 AF XY: 0.233 AC XY: 17348 AN XY: 74366

African (AFR) AF: 0.302 AC: 12545 AN: 41482

American (AMR) AF: 0.250 AC: 3818 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3472

East Asian (EAS) AF: 0.306 AC: 1578 AN: 5152

South Asian (SAS) AF: 0.279 AC: 1346 AN: 4828

European-Finnish (FIN) AF: 0.275 AC: 2906 AN: 10578

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10953 AN: 67986

Other (OTH) AF: 0.184 AC: 388 AN: 2112

Alfa AF: 0.177 Hom.: 11675

Bravo AF: 0.225

Asia WGS AF: 0.263 AC: 911 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs10201616; hg19: chr2-75675860;