rs6457730

Positions:

• chr6-33518955-G-A
• chr6-33518955-G-C

Variant summary

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

The variant allele was found at a frequency of 0.0378 in 151,626 control chromosomes in the GnomAD database, including 268 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 0.038 (268 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.33518955G>A		intergenic_region
LOC107986537	XR_001743876.1	n.144+410C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0377 AC: 5719 AN: 151508 Hom.: 265 Cov.: 30

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.00732

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.00199

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00877

Gnomad OTH AF: 0.0346

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

GnomAD4 genome AF: 0.0378 AC: 5735 AN: 151626 Hom.: 268 Cov.: 30 AF XY: 0.0377 AC XY: 2792 AN XY: 74106

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.00733

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.00199

Gnomad4 NFE AF: 0.00877

Gnomad4 OTH AF: 0.0343

Alfa AF: 0.0154 Hom.: 27

Bravo AF: 0.0442

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.61
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6457730; hg19: chr6-33486732;