chr7-56619180-C-T

Variant names:

• chr7-56619180-C-T
• rs6945964
• ENST00000796931.1:n.280-3765G>A

Variant summary

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

The ENST00000796931.1(ENSG00000287019):​n.280-3765G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 150,690 control chromosomes in the GnomAD database, including 2,432 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 0.18 (2432 hom., cov: 32)
• Consequence: ENSG00000287019 ENST00000796931.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 2 publications found

Genes affected

ENSG00000287019 (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 (AMR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796931.1. 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
	ENSG00000287019	ENST00000796931.1		n.280-3765G>A		intron	N/A
	ENSG00000287019	ENST00000796932.1		n.352-3765G>A		intron	N/A
	ENSG00000287019	ENST00000796933.1		n.444-3765G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26672 AN: 150614 Hom.: 2428 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0107

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.170

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.177 AC: 26686 AN: 150690 Hom.: 2432 Cov.: 32 AF XY: 0.176 AC XY: 12965 AN XY: 73548

African (AFR) AF: 0.172 AC: 7093 AN: 41190

American (AMR) AF: 0.198 AC: 3005 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3468

East Asian (EAS) AF: 0.0107 AC: 55 AN: 5136

South Asian (SAS) AF: 0.135 AC: 648 AN: 4794

European-Finnish (FIN) AF: 0.175 AC: 1730 AN: 9892

Middle Eastern (MID) AF: 0.176 AC: 50 AN: 284

European-Non Finnish (NFE) AF: 0.191 AC: 12951 AN: 67758

Other (OTH) AF: 0.160 AC: 335 AN: 2096

Alfa AF: 0.185 Hom.: 406

Bravo AF: 0.178

Asia WGS AF: 0.0820 AC: 285 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	8.0
DANN	Benign	0.57
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs6945964; hg19: chr7-56686873;