10-128128210-G-T

Variant names:

• chr10-128128210-G-T
• rs10764754

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 0.342 in 152,092 control chromosomes in the GnomAD database, including 9,080 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 (9080 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.409 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: 0.341 AC: 51890 AN: 151974 Hom.: 9066 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.342 AC: 51947 AN: 152092 Hom.: 9080 Cov.: 33 AF XY: 0.349 AC XY: 25951 AN XY: 74352

African (AFR) AF: 0.329 AC: 13664 AN: 41496

American (AMR) AF: 0.417 AC: 6382 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1325 AN: 3466

East Asian (EAS) AF: 0.406 AC: 2100 AN: 5176

South Asian (SAS) AF: 0.403 AC: 1941 AN: 4818

European-Finnish (FIN) AF: 0.383 AC: 4045 AN: 10558

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21255 AN: 67970

Other (OTH) AF: 0.367 AC: 775 AN: 2110

Alfa AF: 0.191 Hom.: 378

Bravo AF: 0.348

Asia WGS AF: 0.402 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.43
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10764754; hg19: chr10-129926474;