5-7227934-C-T

Variant names:

• chr5-7227934-C-T
• rs7729273
• ENST00000650863.1:n.270-387G>A

Variant summary

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

The ENST00000650863.1(ENSG00000286254):​n.270-387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,052 control chromosomes in the GnomAD database, including 2,686 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 0.17 (2686 hom., cov: 32)
• Consequence: ENSG00000286254 ENST00000650863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 7 publications found

Genes affected

ENSG00000286254 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900935	XR_007058682.1	n.1561-387G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286254	ENST00000650863.1	n.270-387G>A		intron_variant	Intron 1 of 1
ENSG00000308577	ENST00000835169.1	n.123+22705G>A		intron_variant	Intron 1 of 2
ENSG00000308577	ENST00000835170.1	n.96+22705G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26182 AN: 151932 Hom.: 2681 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.172 AC: 26196 AN: 152052 Hom.: 2686 Cov.: 32 AF XY: 0.171 AC XY: 12728 AN XY: 74326

African (AFR) AF: 0.0621 AC: 2578 AN: 41490

American (AMR) AF: 0.237 AC: 3616 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3468

East Asian (EAS) AF: 0.155 AC: 801 AN: 5162

South Asian (SAS) AF: 0.150 AC: 720 AN: 4814

European-Finnish (FIN) AF: 0.210 AC: 2221 AN: 10560

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15134 AN: 67960

Other (OTH) AF: 0.175 AC: 369 AN: 2110

Alfa AF: 0.197 Hom.: 7501

Bravo AF: 0.170

Asia WGS AF: 0.136 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.65
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs7729273; hg19: chr5-7228047;