rs2774225

chr6-160280149-G-Achr6-160280149-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105378088 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105378088	XR_001744437.2	n.4524G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.255

Alfa AF: 0.260 Hom.: 1341

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2774225; hg19: chr6-160701181;