ENST00000849450.1:n.638+6615G>A

Variant names:

• chr10-113185119-G-A
• rs11196260
• ENST00000849450.1:n.638+6615G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000849450.1(ENSG00000310382):​n.638+6615G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0245 in 152,280 control chromosomes in the GnomAD database, including 69 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 0.025 (69 hom., cov: 32)
• Consequence: ENSG00000310382 ENST00000849450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 3 publications found

Genes affected

ENSG00000310382 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0245 (3738/152280) while in subpopulation NFE AF = 0.0378 (2568/68020). AF 95% confidence interval is 0.0365. There are 69 homozygotes in GnomAd4. There are 1663 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 69 gene

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
ENSG00000310382	ENST00000849450.1	n.638+6615G>A		intron_variant	Intron 3 of 3
ENSG00000310382	ENST00000849451.1	n.428+6615G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0246 AC: 3741 AN: 152162 Hom.: 69 Cov.: 32

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.00669

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0378

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0245 AC: 3738 AN: 152280 Hom.: 69 Cov.: 32 AF XY: 0.0223 AC XY: 1663 AN XY: 74474

African (AFR) AF: 0.0111 AC: 461 AN: 41558

American (AMR) AF: 0.0178 AC: 273 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0461 AC: 160 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0182 AC: 88 AN: 4822

European-Finnish (FIN) AF: 0.00669 AC: 71 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0378 AC: 2568 AN: 68020

Other (OTH) AF: 0.0318 AC: 67 AN: 2108

Alfa AF: 0.0342 Hom.: 148

Bravo AF: 0.0246

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.70
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs11196260; hg19: chr10-114944878;