rs10501636

Variant names:

• chr11-87401277-T-C
• rs10501636
• ENST00000784851.1:n.475+38801T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-87401277-T-C
• chr11-87401277-T-G

Variant summary

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

The ENST00000784851.1(ENSG00000302190):​n.475+38801T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,080 control chromosomes in the GnomAD database, including 8,178 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 (8178 hom., cov: 32)
• Consequence: ENSG00000302190 ENST00000784851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 4 publications found

Genes affected

ENSG00000302190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784851.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302190	ENST00000784851.1		n.475+38801T>C		intron	N/A
	ENSG00000302212	ENST00000785017.1		n.161+20913A>G		intron	N/A
	ENSG00000302212	ENST00000785018.1		n.284+9453A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45706 AN: 151962 Hom.: 8185 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.0890

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.300 AC: 45687 AN: 152080 Hom.: 8178 Cov.: 32 AF XY: 0.295 AC XY: 21919 AN XY: 74324

African (AFR) AF: 0.124 AC: 5158 AN: 41508

American (AMR) AF: 0.316 AC: 4831 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1476 AN: 3470

East Asian (EAS) AF: 0.0890 AC: 461 AN: 5178

South Asian (SAS) AF: 0.258 AC: 1244 AN: 4816

European-Finnish (FIN) AF: 0.328 AC: 3470 AN: 10580

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27874 AN: 67946

Other (OTH) AF: 0.337 AC: 710 AN: 2106

Alfa AF: 0.333 Hom.: 1640

Bravo AF: 0.293

Asia WGS AF: 0.177 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.52
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10501636; hg19: chr11-87112319;