rs7317940

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr13-77447083-G-A
• chr13-77447083-G-C

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783601.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302049	ENST00000783601.1		n.688-340G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7317940;

hg19: chr13-78021218;