11-49210106-C-T

Variant names:

• chr11-49210106-C-T
• rs647370
• ENST00000759355.1:n.263+1616C>T

Variant summary

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

The ENST00000759355.1(ENSG00000298958):​n.263+1616C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,080 control chromosomes in the GnomAD database, including 9,412 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 0.32 (9412 hom., cov: 32)
• Consequence: ENSG00000298958 ENST00000759355.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775
• Publications: 4 publications found

Genes affected

ENSG00000298958 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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
ENSG00000298958	ENST00000759355.1	n.263+1616C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49361 AN: 151962 Hom.: 9399 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.325 AC: 49412 AN: 152080 Hom.: 9412 Cov.: 32 AF XY: 0.328 AC XY: 24356 AN XY: 74332

African (AFR) AF: 0.532 AC: 22075 AN: 41490

American (AMR) AF: 0.254 AC: 3875 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1667 AN: 5176

South Asian (SAS) AF: 0.355 AC: 1714 AN: 4822

European-Finnish (FIN) AF: 0.297 AC: 3139 AN: 10552

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.229 AC: 15562 AN: 67978

Other (OTH) AF: 0.268 AC: 566 AN: 2114

Alfa AF: 0.284 Hom.: 958

Bravo AF: 0.326

Asia WGS AF: 0.384 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.55
DANN	Benign	0.70
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs647370; hg19: chr11-49231658; COSMIC: COSV57049388;