rs10749418

Variant names:

• chr10-121475547-T-G
• rs10749418

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 0.627 in 152,150 control chromosomes in the GnomAD database, including 33,117 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 0.63 (33117 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 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: 0.628 AC: 95430 AN: 152030 Hom.: 33100 Cov.: 34

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.627 AC: 95471 AN: 152150 Hom.: 33117 Cov.: 34 AF XY: 0.632 AC XY: 46998 AN XY: 74372

African (AFR) AF: 0.319 AC: 13243 AN: 41480

American (AMR) AF: 0.760 AC: 11620 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2683 AN: 3472

East Asian (EAS) AF: 0.381 AC: 1970 AN: 5168

South Asian (SAS) AF: 0.661 AC: 3188 AN: 4820

European-Finnish (FIN) AF: 0.807 AC: 8551 AN: 10594

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52018 AN: 68006

Other (OTH) AF: 0.646 AC: 1365 AN: 2114

Alfa AF: 0.687 Hom.: 15122

Bravo AF: 0.611

Asia WGS AF: 0.535 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.79
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs10749418; hg19: chr10-123235061; COSMIC: COSV61145986;