rs7239116

Variant names:

• chr18-21906764-T-C
• rs7239116
• ENST00000778525.1:n.260-8483T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-21906764-T-C
• chr18-21906764-T-G

Variant summary

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

The ENST00000778525.1(ENSG00000301367):​n.260-8483T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,014 control chromosomes in the GnomAD database, including 14,091 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 0.42 (14091 hom., cov: 32)
• Consequence: ENSG00000301367 ENST00000778525.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• Publications: 4 publications found

Genes affected

ENSG00000301367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372016	XR_935276.3	n.285-719T>C		intron_variant	Intron 1 of 3
LOC105372016	XR_935277.4	n.284-8483T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301367	ENST00000778525.1	n.260-8483T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63418 AN: 151896 Hom.: 14068 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.418 AC: 63501 AN: 152014 Hom.: 14091 Cov.: 32 AF XY: 0.422 AC XY: 31335 AN XY: 74308

African (AFR) AF: 0.557 AC: 23082 AN: 41428

American (AMR) AF: 0.507 AC: 7739 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1296 AN: 3466

East Asian (EAS) AF: 0.416 AC: 2148 AN: 5166

South Asian (SAS) AF: 0.450 AC: 2173 AN: 4828

European-Finnish (FIN) AF: 0.366 AC: 3866 AN: 10556

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21893 AN: 67992

Other (OTH) AF: 0.424 AC: 894 AN: 2108

Alfa AF: 0.362 Hom.: 12711

Bravo AF: 0.432

Asia WGS AF: 0.506 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.71
DANN	Benign	0.69
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7239116; hg19: chr18-19486725;