rs6024619

Variant names:

• chr20-56102894-G-A
• rs6024619
• XR_936891.1:n.161G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-56102894-G-A
• chr20-56102894-G-C
• chr20-56102894-G-T

Variant summary

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

The XR_936891.1(LOC105376989):​n.161G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,972 control chromosomes in the GnomAD database, including 11,507 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 0.35 (11507 hom., cov: 32)
• Consequence: LOC105376989 XR_936891.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994
• Publications: 3 publications found

Genes affected

LOC105376989 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 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: 0.351 AC: 53275 AN: 151854 Hom.: 11477 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.351 AC: 53352 AN: 151972 Hom.: 11507 Cov.: 32 AF XY: 0.349 AC XY: 25915 AN XY: 74274

African (AFR) AF: 0.611 AC: 25319 AN: 41442

American (AMR) AF: 0.235 AC: 3587 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3468

East Asian (EAS) AF: 0.458 AC: 2353 AN: 5142

South Asian (SAS) AF: 0.301 AC: 1450 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3036 AN: 10552

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16147 AN: 67956

Other (OTH) AF: 0.294 AC: 621 AN: 2110

Alfa AF: 0.250 Hom.: 4553

Bravo AF: 0.360

Asia WGS AF: 0.422 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs6024619; hg19: chr20-54677950;