chr7-76301483-G-A

Variant names:

• chr7-76301483-G-A
• rs2868370
• ENST00000740305.1:n.238G>A

Variant summary

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

The ENST00000740305.1(ENSG00000296557):​n.238G>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 0.156 in 151,592 control chromosomes in the GnomAD database, including 2,048 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 0.16 (2048 hom., cov: 32)
• Consequence: ENSG00000296557 ENST00000740305.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• Publications: 11 publications found

Genes affected

ENSG00000296557 (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 (AMR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740305.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000296557	ENST00000740305.1		n.238G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000296557	ENST00000740306.1		n.196-1119G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23576 AN: 151484 Hom.: 2049 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0987

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.156 AC: 23574 AN: 151592 Hom.: 2048 Cov.: 32 AF XY: 0.159 AC XY: 11758 AN XY: 73994

African (AFR) AF: 0.101 AC: 4180 AN: 41398

American (AMR) AF: 0.184 AC: 2794 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.0987 AC: 342 AN: 3466

East Asian (EAS) AF: 0.183 AC: 943 AN: 5154

South Asian (SAS) AF: 0.119 AC: 573 AN: 4808

European-Finnish (FIN) AF: 0.289 AC: 2989 AN: 10352

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.168 AC: 11428 AN: 67922

Other (OTH) AF: 0.138 AC: 289 AN: 2100

Alfa AF: 0.163 Hom.: 256

Bravo AF: 0.148

Asia WGS AF: 0.174 AC: 605 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	4.9
DANN	Benign	0.48
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs2868370; hg19: chr7-75930800;