rs2774225

Variant names:

• chr6-160280149-G-A
• rs2774225
• XR_001744437.2:n.4524G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-160280149-G-A
• chr6-160280149-G-C

Variant summary

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

The XR_001744437.2(LOC105378088):​n.4524G>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 0.276 in 152,122 control chromosomes in the GnomAD database, including 5,915 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 0.28 (5915 hom., cov: 33)
• Consequence: LOC105378088 XR_001744437.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 3 publications found

Genes affected

LOC105378088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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: 0.276 AC: 41931 AN: 152006 Hom.: 5897 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.208

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.276 AC: 41981 AN: 152122 Hom.: 5915 Cov.: 33 AF XY: 0.278 AC XY: 20649 AN XY: 74404

African (AFR) AF: 0.322 AC: 13369 AN: 41480

American (AMR) AF: 0.256 AC: 3911 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3468

East Asian (EAS) AF: 0.178 AC: 924 AN: 5182

South Asian (SAS) AF: 0.287 AC: 1385 AN: 4820

European-Finnish (FIN) AF: 0.288 AC: 3052 AN: 10592

Middle Eastern (MID) AF: 0.200 AC: 58 AN: 290

European-Non Finnish (NFE) AF: 0.260 AC: 17674 AN: 67972

Other (OTH) AF: 0.255 AC: 540 AN: 2114

Alfa AF: 0.259 Hom.: 2367

Bravo AF: 0.277

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs2774225; hg19: chr6-160701181;