chr10-121700564-C-T

Variant names:

• chr10-121700564-C-T
• rs7900009

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 0.471 in 151,938 control chromosomes in the GnomAD database, including 18,206 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 0.47 (18206 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.471 AC: 71551 AN: 151820 Hom.: 18203 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.471 AC: 71564 AN: 151938 Hom.: 18206 Cov.: 32 AF XY: 0.477 AC XY: 35412 AN XY: 74280

African (AFR) AF: 0.271 AC: 11210 AN: 41410

American (AMR) AF: 0.467 AC: 7131 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2102 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2138 AN: 5146

South Asian (SAS) AF: 0.544 AC: 2611 AN: 4802

European-Finnish (FIN) AF: 0.619 AC: 6544 AN: 10576

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 38001 AN: 67954

Other (OTH) AF: 0.475 AC: 1001 AN: 2108

Alfa AF: 0.508 Hom.: 7451

Bravo AF: 0.446

Asia WGS AF: 0.456 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.6
DANN	Benign	0.79
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7900009; hg19: chr10-123460078;