10-95032445-T-C

Variant names:

• chr10-95032445-T-C
• rs1934954

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 0.0554 in 152,248 control chromosomes in the GnomAD database, including 303 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 0.055 (303 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.078 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: 0.0554 AC: 8432 AN: 152130 Hom.: 303 Cov.: 33

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0797

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0554 AC: 8429 AN: 152248 Hom.: 303 Cov.: 33 AF XY: 0.0537 AC XY: 3995 AN XY: 74436

African (AFR) AF: 0.0160 AC: 665 AN: 41544

American (AMR) AF: 0.0741 AC: 1134 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3468

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.0262 AC: 126 AN: 4818

European-Finnish (FIN) AF: 0.0625 AC: 663 AN: 10604

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0797 AC: 5422 AN: 68000

Other (OTH) AF: 0.0715 AC: 151 AN: 2112

Alfa AF: 0.0632 Hom.: 196

Bravo AF: 0.0556

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.59
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1934954; hg19: chr10-96792202;