rs6507945

Variant names:

• chr18-49717542-A-C
• rs6507945
• ENST00000849189.1:n.712+17185A>C

Your query was ambiguous. Multiple possible variants found:

• chr18-49717542-A-C
• chr18-49717542-A-T

Variant summary

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

The ENST00000849189.1(ENSG00000310339):​n.712+17185A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,622 control chromosomes in the GnomAD database, including 28,595 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 0.60 (28595 hom., cov: 31)
• Consequence: ENSG00000310339 ENST00000849189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989
• Publications: 12 publications found

Genes affected

ENSG00000310339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372112	XR_007066363.1	n.642+17185A>C		intron_variant	Intron 3 of 4
LOC105372112	XR_007066364.1	n.887+17185A>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310339	ENST00000849189.1	n.712+17185A>C		intron_variant	Intron 3 of 3
ENSG00000310339	ENST00000849190.1	n.404+17185A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91545 AN: 151514 Hom.: 28561 Cov.: 31

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.604 AC: 91628 AN: 151622 Hom.: 28595 Cov.: 31 AF XY: 0.599 AC XY: 44364 AN XY: 74070

African (AFR) AF: 0.776 AC: 32120 AN: 41380

American (AMR) AF: 0.506 AC: 7711 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3468

East Asian (EAS) AF: 0.366 AC: 1884 AN: 5146

South Asian (SAS) AF: 0.564 AC: 2715 AN: 4810

European-Finnish (FIN) AF: 0.500 AC: 5173 AN: 10342

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38195 AN: 67912

Other (OTH) AF: 0.599 AC: 1261 AN: 2106

Alfa AF: 0.574 Hom.: 98377

Bravo AF: 0.609

Asia WGS AF: 0.500 AC: 1740 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.35
DANN	Benign	0.41
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs6507945; hg19: chr18-47243912;