7-122229305-T-C

Variant names:

• chr7-122229305-T-C
• rs570501
• ENST00000718494.1:n.267+27909T>C

Variant summary

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

The ENST00000718494.1(ENSG00000293696):​n.267+27909T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,064 control chromosomes in the GnomAD database, including 41,908 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 0.73 (41908 hom., cov: 32)
• Consequence: ENSG00000293696 ENST00000718494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 1 publications found

Genes affected

ENSG00000293696 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718494.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293696	ENST00000718494.1		n.267+27909T>C		intron	N/A
	ENSG00000308663	ENST00000835595.1		n.507-8909A>G		intron	N/A
	ENSG00000308663	ENST00000835596.1		n.338-8909A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111365 AN: 151944 Hom.: 41879 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.733 AC: 111437 AN: 152064 Hom.: 41908 Cov.: 32 AF XY: 0.734 AC XY: 54604 AN XY: 74348

African (AFR) AF: 0.548 AC: 22685 AN: 41424

American (AMR) AF: 0.795 AC: 12147 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2578 AN: 3470

East Asian (EAS) AF: 0.744 AC: 3836 AN: 5158

South Asian (SAS) AF: 0.771 AC: 3719 AN: 4826

European-Finnish (FIN) AF: 0.876 AC: 9294 AN: 10610

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54590 AN: 67978

Other (OTH) AF: 0.757 AC: 1599 AN: 2112

Alfa AF: 0.769 Hom.: 15499

Bravo AF: 0.717

Asia WGS AF: 0.781 AC: 2710 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.45
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs570501; hg19: chr7-121869359;