7-23561605-T-G

Variant names:

• chr7-23561605-T-G
• rs227940
• ENST00000725513.1:n.188-1917T>G

Variant summary

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

The ENST00000725513.1(ENSG00000294729):​n.188-1917T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,860 control chromosomes in the GnomAD database, including 18,945 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 0.50 (18945 hom., cov: 32)
• Consequence: ENSG00000294729 ENST00000725513.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.716
• Publications: 9 publications found

Genes affected

ENSG00000294729 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725513.1. 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
	ENSG00000294729	ENST00000725513.1		n.188-1917T>G		intron	N/A
	ENSG00000294729	ENST00000725514.1		n.188-1917T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75295 AN: 151742 Hom.: 18952 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.496 AC: 75313 AN: 151860 Hom.: 18945 Cov.: 32 AF XY: 0.504 AC XY: 37372 AN XY: 74200

African (AFR) AF: 0.422 AC: 17485 AN: 41450

American (AMR) AF: 0.531 AC: 8095 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1785 AN: 3472

East Asian (EAS) AF: 0.686 AC: 3538 AN: 5160

South Asian (SAS) AF: 0.616 AC: 2969 AN: 4818

European-Finnish (FIN) AF: 0.558 AC: 5877 AN: 10524

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33829 AN: 67872

Other (OTH) AF: 0.477 AC: 1007 AN: 2112

Alfa AF: 0.503 Hom.: 80392

Bravo AF: 0.493

Asia WGS AF: 0.631 AC: 2182 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs227940; hg19: chr7-23601224;