11-61975806-T-C

Variant names:

• chr11-61975806-T-C
• rs17156616
• ENST00000796889.1:n.184+8285T>C

Variant summary

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

The ENST00000796889.1(ENSG00000303745):​n.184+8285T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,212 control chromosomes in the GnomAD database, including 2,683 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 0.15 (2683 hom., cov: 33)
• Consequence: ENSG00000303745 ENST00000796889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 1 publications found

Genes affected

ENSG00000303745 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796889.1. 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
	ENSG00000303745	ENST00000796889.1		n.184+8285T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22786 AN: 152094 Hom.: 2677 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.150 AC: 22809 AN: 152212 Hom.: 2683 Cov.: 33 AF XY: 0.157 AC XY: 11710 AN XY: 74414

African (AFR) AF: 0.199 AC: 8279 AN: 41522

American (AMR) AF: 0.181 AC: 2764 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3472

East Asian (EAS) AF: 0.652 AC: 3368 AN: 5164

South Asian (SAS) AF: 0.143 AC: 690 AN: 4826

European-Finnish (FIN) AF: 0.149 AC: 1577 AN: 10602

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0832 AC: 5661 AN: 68022

Other (OTH) AF: 0.126 AC: 266 AN: 2116

Alfa AF: 0.122 Hom.: 2906

Bravo AF: 0.159

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	13
DANN	Benign	0.77
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs17156616; hg19: chr11-61743278;