rs10499638

Variant names:

• chr7-46127333-A-C
• rs10499638
• ENST00000796919.1:n.243-665A>C

Variant summary

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

The ENST00000796919.1(ENSG00000303748):​n.243-665A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,106 control chromosomes in the GnomAD database, including 3,297 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 0.18 (3297 hom., cov: 32)
• Consequence: ENSG00000303748 ENST00000796919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 6 publications found

Genes affected

ENSG00000303748 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 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
ENSG00000303748	ENST00000796919.1	n.243-665A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27481 AN: 151992 Hom.: 3296 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.181 AC: 27482 AN: 152106 Hom.: 3297 Cov.: 32 AF XY: 0.182 AC XY: 13567 AN XY: 74340

African (AFR) AF: 0.0473 AC: 1966 AN: 41528

American (AMR) AF: 0.269 AC: 4112 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 359 AN: 3468

East Asian (EAS) AF: 0.0170 AC: 88 AN: 5172

South Asian (SAS) AF: 0.119 AC: 574 AN: 4818

European-Finnish (FIN) AF: 0.316 AC: 3328 AN: 10538

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16507 AN: 67986

Other (OTH) AF: 0.162 AC: 342 AN: 2106

Alfa AF: 0.226 Hom.: 1869

Bravo AF: 0.173

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.53
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs10499638; hg19: chr7-46166931;