rs4748699

Variant names:

• chr10-20695978-G-A
• rs4748699

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 0.133 in 152,096 control chromosomes in the GnomAD database, including 1,601 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 0.13 (1601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.241 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: 0.133 AC: 20191 AN: 151978 Hom.: 1592 Cov.: 32

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.133 AC: 20215 AN: 152096 Hom.: 1601 Cov.: 32 AF XY: 0.133 AC XY: 9918 AN XY: 74336

African (AFR) AF: 0.0642 AC: 2667 AN: 41510

American (AMR) AF: 0.147 AC: 2241 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3468

East Asian (EAS) AF: 0.191 AC: 983 AN: 5160

South Asian (SAS) AF: 0.252 AC: 1217 AN: 4822

European-Finnish (FIN) AF: 0.105 AC: 1113 AN: 10580

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10573 AN: 67968

Other (OTH) AF: 0.167 AC: 351 AN: 2108

Alfa AF: 0.159 Hom.: 3356

Bravo AF: 0.134

Asia WGS AF: 0.224 AC: 780 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	2.5
DANN	Benign	0.60
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs4748699; hg19: chr10-20984907;