rs1338799

Variant names:

• chr10-55869919-T-C
• rs1338799
• ENST00000837206.1:n.317-29440A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000837206.1(ENSG00000308905):​n.317-29440A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,048 control chromosomes in the GnomAD database, including 7,765 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 0.30 (7765 hom., cov: 32)
• Consequence: ENSG00000308905 ENST00000837206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 3 publications found

Genes affected

ENSG00000308905 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 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
ENSG00000308905	ENST00000837206.1	n.317-29440A>G		intron_variant	Intron 2 of 2
ENSG00000308905	ENST00000837207.1	n.457-29440A>G		intron_variant	Intron 1 of 1
ENSG00000308905	ENST00000837208.1	n.312-29440A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45762 AN: 151930 Hom.: 7771 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.301 AC: 45757 AN: 152048 Hom.: 7765 Cov.: 32 AF XY: 0.297 AC XY: 22086 AN XY: 74330

African (AFR) AF: 0.160 AC: 6624 AN: 41502

American (AMR) AF: 0.275 AC: 4205 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3468

East Asian (EAS) AF: 0.386 AC: 1984 AN: 5142

South Asian (SAS) AF: 0.316 AC: 1526 AN: 4822

European-Finnish (FIN) AF: 0.274 AC: 2896 AN: 10576

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.384 AC: 26111 AN: 67958

Other (OTH) AF: 0.306 AC: 646 AN: 2114

Alfa AF: 0.340 Hom.: 1168

Bravo AF: 0.295

Asia WGS AF: 0.324 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1338799; hg19: chr10-57629679;