7-88714509-T-C

Variant names:

• chr7-88714509-T-C
• rs10487032
• ENST00000444032.1:n.65+3814T>C

Variant summary

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

The ENST00000444032.1(ENSG00000233420):​n.65+3814T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 152,260 control chromosomes in the GnomAD database, including 285 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 0.037 (285 hom., cov: 32)
• Consequence: ENSG00000233420 ENST00000444032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 1 publications found

Genes affected

ENSG00000233420 (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 (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986816	XR_001745261.2	n.423+17711T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233420	ENST00000444032.1	n.65+3814T>C		intron_variant	Intron 1 of 5	3
ENSG00000233420	ENST00000663862.1	n.460-27508T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0366 AC: 5565 AN: 152142 Hom.: 285 Cov.: 32

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.0372

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

GnomAD4 genome AF: 0.0366 AC: 5566 AN: 152260 Hom.: 285 Cov.: 32 AF XY: 0.0390 AC XY: 2906 AN XY: 74456

African (AFR) AF: 0.0257 AC: 1069 AN: 41552

American (AMR) AF: 0.0761 AC: 1164 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1371 AN: 5178

South Asian (SAS) AF: 0.0255 AC: 123 AN: 4828

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10608

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0213 AC: 1449 AN: 68016

Other (OTH) AF: 0.0378 AC: 80 AN: 2116

Alfa AF: 0.0150 Hom.: 13

Bravo AF: 0.0413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.48
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10487032; hg19: chr7-88343823;