rs738134

Positions:

• chr7-130782816-C-G
• chr7-130782816-C-T

Variant summary

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

The XR_927976.3(LOC105375508):​n.179-4C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,098 control chromosomes in the GnomAD database, including 8,205 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 0.32 (8205 hom., cov: 33)
• Consequence: LOC105375508 XR_927976.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.130782816C>G		intergenic_region
LOC105375508	XR_007060527.1	n.179-4C>G		splice_region_variant, intron_variant
LOC105375508	XR_927976.3	n.179-4C>G		splice_region_variant, intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49158 AN: 151978 Hom.: 8209 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.323 AC: 49155 AN: 152098 Hom.: 8205 Cov.: 33 AF XY: 0.326 AC XY: 24221 AN XY: 74358

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.317

Alfa AF: 0.204 Hom.: 448

Bravo AF: 0.330

Asia WGS AF: 0.382 AC: 1324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs738134; hg19: chr7-130467575;