rs1248993

Variant names:

• chr10-28738294-A-G
• rs1248993

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 0.139 in 152,116 control chromosomes in the GnomAD database, including 1,971 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 0.14 (1971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.139 AC: 21067 AN: 151998 Hom.: 1966 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.0841

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0914

Gnomad FIN AF: 0.0728

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.139 AC: 21088 AN: 152116 Hom.: 1971 Cov.: 32 AF XY: 0.134 AC XY: 9978 AN XY: 74390

African (AFR) AF: 0.274 AC: 11347 AN: 41458

American (AMR) AF: 0.0840 AC: 1283 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3470

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5170

South Asian (SAS) AF: 0.0917 AC: 442 AN: 4820

European-Finnish (FIN) AF: 0.0728 AC: 772 AN: 10598

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0946 AC: 6436 AN: 68016

Other (OTH) AF: 0.120 AC: 253 AN: 2112

Alfa AF: 0.120 Hom.: 2663

Bravo AF: 0.144

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.83
DANN	Benign	0.61
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1248993; hg19: chr10-29027223;