chr5-1295957-A-G

Variant names:

• chr5-1295957-A-G
• rs7712562
• ENST00000771252.1:n.276A>G

Variant summary

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

The ENST00000771252.1(ENSG00000300381):​n.276A>G 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 0.884 in 152,240 control chromosomes in the GnomAD database, including 59,662 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 0.88 (59662 hom., cov: 33)
• Consequence: ENSG00000300381 ENST00000771252.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 19 publications found

Genes affected

ENSG00000300381 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300381	ENST00000771252.1	n.276A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134433 AN: 152122 Hom.: 59590 Cov.: 33

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.884 AC: 134566 AN: 152240 Hom.: 59662 Cov.: 33 AF XY: 0.884 AC XY: 65797 AN XY: 74440

African (AFR) AF: 0.952 AC: 39575 AN: 41566

American (AMR) AF: 0.879 AC: 13456 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2797 AN: 3470

East Asian (EAS) AF: 0.895 AC: 4617 AN: 5156

South Asian (SAS) AF: 0.905 AC: 4369 AN: 4828

European-Finnish (FIN) AF: 0.843 AC: 8936 AN: 10604

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 57987 AN: 67996

Other (OTH) AF: 0.852 AC: 1803 AN: 2116

Alfa AF: 0.854 Hom.: 25261

Bravo AF: 0.889

Asia WGS AF: 0.918 AC: 3189 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.38
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs7712562; hg19: chr5-1296072;