chr7-128223952-G-A

Variant names:

• chr7-128223952-G-A
• rs10954172
• ENST00000690022.2:n.289-2412C>T

Variant summary

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

The ENST00000690022.2(ENSG00000289434):​n.289-2412C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,018 control chromosomes in the GnomAD database, including 6,089 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 0.26 (6089 hom., cov: 31)
• Consequence: ENSG00000289434 ENST00000690022.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 2 publications found

Genes affected

ENSG00000289434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901744	XR_007060516.1	n.781-81G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289434	ENST00000690022.2	n.289-2412C>T		intron_variant	Intron 2 of 2
ENSG00000289434	ENST00000692614.3	n.528-2412C>T		intron_variant	Intron 2 of 2
ENSG00000292309	ENST00000710955.1	n.836-81G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39852 AN: 151900 Hom.: 6082 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.262 AC: 39883 AN: 152018 Hom.: 6089 Cov.: 31 AF XY: 0.264 AC XY: 19602 AN XY: 74296

African (AFR) AF: 0.117 AC: 4862 AN: 41466

American (AMR) AF: 0.383 AC: 5851 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3472

East Asian (EAS) AF: 0.173 AC: 893 AN: 5168

South Asian (SAS) AF: 0.312 AC: 1500 AN: 4814

European-Finnish (FIN) AF: 0.278 AC: 2931 AN: 10554

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21686 AN: 67966

Other (OTH) AF: 0.259 AC: 544 AN: 2102

Alfa AF: 0.299 Hom.: 27911

Bravo AF: 0.266

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.55
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10954172; hg19: chr7-127864005;