7-128217838-G-T

Variant names:

• chr7-128217838-G-T
• rs2167289
• ENST00000710955.1:n.836-6195G>T

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.836-6195G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,110 control chromosomes in the GnomAD database, including 10,216 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 0.35 (10216 hom., cov: 33)
• Consequence: ENSG00000292309 ENST00000710955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.40
• Publications: 13 publications found

Genes affected

ENSG00000292309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000710955.1. 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
	ENSG00000292309	ENST00000710955.1		n.836-6195G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52492 AN: 151992 Hom.: 10213 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.345 AC: 52510 AN: 152110 Hom.: 10216 Cov.: 33 AF XY: 0.348 AC XY: 25890 AN XY: 74338

African (AFR) AF: 0.176 AC: 7321 AN: 41518

American (AMR) AF: 0.360 AC: 5512 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3470

East Asian (EAS) AF: 0.660 AC: 3407 AN: 5166

South Asian (SAS) AF: 0.328 AC: 1583 AN: 4828

European-Finnish (FIN) AF: 0.445 AC: 4689 AN: 10542

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27418 AN: 67976

Other (OTH) AF: 0.373 AC: 788 AN: 2114

Alfa AF: 0.385 Hom.: 49242

Bravo AF: 0.331

Asia WGS AF: 0.489 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs2167289; hg19: chr7-127857891;