7-56119414-A-G

Variant names:

• chr7-56119414-A-G
• rs816417
• ENST00000836569.1:n.294+2615A>G

Variant summary

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

The ENST00000836569.1(ENSG00000308815):​n.294+2615A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,112 control chromosomes in the GnomAD database, including 10,164 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 0.36 (10164 hom., cov: 33)
• Consequence: ENSG00000308815 ENST00000836569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 2 publications found

Genes affected

ENSG00000308815 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836569.1. 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
	ENSG00000308815	ENST00000836569.1		n.294+2615A>G		intron	N/A
	ENSG00000308815	ENST00000836570.1		n.294+2615A>G		intron	N/A
	ENSG00000308815	ENST00000836571.1		n.287+2615A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55213 AN: 151994 Hom.: 10160 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.363 AC: 55257 AN: 152112 Hom.: 10164 Cov.: 33 AF XY: 0.364 AC XY: 27049 AN XY: 74394

African (AFR) AF: 0.406 AC: 16849 AN: 41478

American (AMR) AF: 0.340 AC: 5184 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1216 AN: 3472

East Asian (EAS) AF: 0.244 AC: 1263 AN: 5186

South Asian (SAS) AF: 0.452 AC: 2180 AN: 4824

European-Finnish (FIN) AF: 0.322 AC: 3408 AN: 10584

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.353 AC: 24035 AN: 67994

Other (OTH) AF: 0.330 AC: 695 AN: 2108

Alfa AF: 0.356 Hom.: 1203

Bravo AF: 0.362

Asia WGS AF: 0.357 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.77
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs816417; hg19: chr7-56187107;