10-69778536-C-T

Variant names:

• chr10-69778536-C-T
• rs4746003

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 0.249 in 151,874 control chromosomes in the GnomAD database, including 4,778 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 0.25 (4778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.249 AC: 37781 AN: 151758 Hom.: 4768 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.249 AC: 37819 AN: 151874 Hom.: 4778 Cov.: 32 AF XY: 0.250 AC XY: 18576 AN XY: 74220

African (AFR) AF: 0.265 AC: 10991 AN: 41432

American (AMR) AF: 0.217 AC: 3316 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3464

East Asian (EAS) AF: 0.229 AC: 1181 AN: 5164

South Asian (SAS) AF: 0.201 AC: 966 AN: 4798

European-Finnish (FIN) AF: 0.269 AC: 2832 AN: 10524

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.247 AC: 16748 AN: 67924

Other (OTH) AF: 0.248 AC: 521 AN: 2102

Alfa AF: 0.249 Hom.: 15607

Bravo AF: 0.249

Asia WGS AF: 0.228 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.65
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs4746003; hg19: chr10-71538292;