rs6507945

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007066363.1(LOC105372112):​n.642+17185A>C variant causes a intron, non coding transcript 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: LOC105372112 XR_007066363.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989

Genes affected

LOC105372112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105372112	XR_007066363.1	n.642+17185A>C		intron_variant, non_coding_transcript_variant
LOC105372112	XR_007066364.1	n.887+17185A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.599

Alfa AF: 0.564 Hom.: 41403

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6507945; hg19: chr18-47243912;