rs6427595

Variant names:

• chr1-161493708-G-A
• rs6427595
• XR_922214.3:n.1903+89G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-161493708-G-A
• chr1-161493708-G-T

Variant summary

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

The XR_922214.3(LOC105371473):​n.1903+89G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,146 control chromosomes in the GnomAD database, including 42,246 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 0.74 (42246 hom., cov: 32)
• Consequence: LOC105371473 XR_922214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 7 publications found

Genes affected

LOC105371473 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.761 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: 0.738 AC: 112180 AN: 152026 Hom.: 42219 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.738 AC: 112264 AN: 152146 Hom.: 42246 Cov.: 32 AF XY: 0.733 AC XY: 54464 AN XY: 74352

African (AFR) AF: 0.755 AC: 31344 AN: 41498

American (AMR) AF: 0.770 AC: 11774 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2809 AN: 3472

East Asian (EAS) AF: 0.282 AC: 1458 AN: 5174

South Asian (SAS) AF: 0.542 AC: 2608 AN: 4812

European-Finnish (FIN) AF: 0.725 AC: 7672 AN: 10582

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52151 AN: 67994

Other (OTH) AF: 0.730 AC: 1540 AN: 2110

Alfa AF: 0.710 Hom.: 4817

Bravo AF: 0.746

Asia WGS AF: 0.454 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.68
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6427595; hg19: chr1-161463498;