chr13-77447083-G-A

Variant names:

• chr13-77447083-G-A
• rs7317940
• ENST00000783601.1:n.688-340G>A

Variant summary

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

The ENST00000783601.1(ENSG00000302049):​n.688-340G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,174 control chromosomes in the GnomAD database, including 5,054 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 0.24 (5054 hom., cov: 32)
• Consequence: ENSG00000302049 ENST00000783601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• Publications: 5 publications found

Genes affected

ENSG00000302049 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903186	XR_007063828.1	n.94-5332G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302049	ENST00000783601.1	n.688-340G>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36125 AN: 152056 Hom.: 5043 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.238 AC: 36149 AN: 152174 Hom.: 5054 Cov.: 32 AF XY: 0.237 AC XY: 17660 AN XY: 74396

African (AFR) AF: 0.106 AC: 4408 AN: 41538

American (AMR) AF: 0.252 AC: 3848 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3470

East Asian (EAS) AF: 0.0703 AC: 365 AN: 5192

South Asian (SAS) AF: 0.292 AC: 1407 AN: 4820

European-Finnish (FIN) AF: 0.310 AC: 3278 AN: 10584

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21133 AN: 67972

Other (OTH) AF: 0.225 AC: 475 AN: 2114

Alfa AF: 0.280 Hom.: 20809

Bravo AF: 0.224

Asia WGS AF: 0.177 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.20
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs7317940; hg19: chr13-78021218;