7-95695555-T-A

Variant names:

• chr7-95695555-T-A
• rs6465475
• ENST00000787388.1:n.233-21552T>A

Variant summary

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

The ENST00000787388.1(ENSG00000302505):​n.233-21552T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,506 control chromosomes in the GnomAD database, including 7,209 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 (7209 hom., cov: 32)
• Consequence: ENSG00000302505 ENST00000787388.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 0 publications found

Genes affected

ENSG00000302505 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787388.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302505	ENST00000787388.1		n.233-21552T>A		intron	N/A
	ENSG00000302505	ENST00000787391.1		n.178-21552T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41942 AN: 151388 Hom.: 7193 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.277 AC: 42003 AN: 151506 Hom.: 7209 Cov.: 32 AF XY: 0.272 AC XY: 20148 AN XY: 74062

African (AFR) AF: 0.494 AC: 20380 AN: 41258

American (AMR) AF: 0.190 AC: 2891 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3464

East Asian (EAS) AF: 0.0627 AC: 322 AN: 5132

South Asian (SAS) AF: 0.260 AC: 1251 AN: 4816

European-Finnish (FIN) AF: 0.156 AC: 1643 AN: 10560

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.205 AC: 13886 AN: 67758

Other (OTH) AF: 0.276 AC: 579 AN: 2098

Alfa AF: 0.103 Hom.: 140

Bravo AF: 0.287

Asia WGS AF: 0.162 AC: 563 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.60
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs6465475; hg19: chr7-95324867;