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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378088	XR_001744437.2	n.4524G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;