7-17957989-T-C

Variant names:

• chr7-17957989-T-C
• rs10226084
• ENST00000817266.1:n.352-681T>C

Variant summary

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

The ENST00000817266.1(ENSG00000306369):​n.352-681T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,968 control chromosomes in the GnomAD database, including 16,420 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 0.46 (16420 hom., cov: 32)
• Consequence: ENSG00000306369 ENST00000817266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 11 publications found

Genes affected

ENSG00000306369 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000817266.1. 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
	ENSG00000306369	ENST00000817266.1		n.352-681T>C		intron	N/A
	ENSG00000306369	ENST00000817267.1		n.297-681T>C		intron	N/A
	ENSG00000306369	ENST00000817268.1		n.256-681T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69581 AN: 151854 Hom.: 16401 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.458 AC: 69649 AN: 151968 Hom.: 16420 Cov.: 32 AF XY: 0.462 AC XY: 34333 AN XY: 74272

African (AFR) AF: 0.384 AC: 15923 AN: 41450

American (AMR) AF: 0.508 AC: 7762 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1699 AN: 5164

South Asian (SAS) AF: 0.294 AC: 1419 AN: 4820

European-Finnish (FIN) AF: 0.616 AC: 6494 AN: 10542

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33441 AN: 67930

Other (OTH) AF: 0.457 AC: 966 AN: 2112

Alfa AF: 0.463 Hom.: 26247

Bravo AF: 0.451

Asia WGS AF: 0.318 AC: 1106 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.42
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs10226084; hg19: chr7-17997612;