rs6457730

Variant names:

• chr6-33518955-G-A
• rs6457730
• XR_001743876.1:n.144+410C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The XR_001743876.1(LOC107986537):​n.144+410C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: LOC107986537 XR_001743876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 4 publications found

Genes affected

LOC107986537 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.108 AC: 4462 AN: 41152

American (AMR) AF: 0.0225 AC: 342 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3472

East Asian (EAS) AF: 0.00733 AC: 38 AN: 5182

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4798

European-Finnish (FIN) AF: 0.00199 AC: 21 AN: 10572

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00877 AC: 596 AN: 67960

Other (OTH) AF: 0.0343 AC: 72 AN: 2100

Alfa AF: 0.0190 Hom.: 52

Bravo AF: 0.0442

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.61
DANN	Benign	0.51
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6457730; hg19: chr6-33486732;