ENST00000658032.1:n.331-42124G>A

Variant names:

• chr7-110407414-C-T
• rs6968385
• ENST00000658032.1:n.331-42124G>A

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.331-42124G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,748 control chromosomes in the GnomAD database, including 15,512 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 0.45 (15512 hom., cov: 31)
• Consequence: ENSG00000226965 ENST00000658032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 9 publications found

Genes affected

ENSG00000226965 (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 (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375451	XR_927863.3	n.386+25397G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226965	ENST00000658032.1	n.331-42124G>A		intron_variant	Intron 3 of 5
ENSG00000226965	ENST00000666128.1	n.97+25397G>A		intron_variant	Intron 2 of 3
ENSG00000226965	ENST00000667232.1	n.411+25397G>A		intron_variant	Intron 4 of 7
ENSG00000226965	ENST00000843035.1	n.351+25397G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68123 AN: 151628 Hom.: 15485 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.449 AC: 68196 AN: 151748 Hom.: 15512 Cov.: 31 AF XY: 0.451 AC XY: 33415 AN XY: 74128

African (AFR) AF: 0.457 AC: 18897 AN: 41372

American (AMR) AF: 0.451 AC: 6852 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1422 AN: 3460

East Asian (EAS) AF: 0.628 AC: 3236 AN: 5154

South Asian (SAS) AF: 0.568 AC: 2737 AN: 4816

European-Finnish (FIN) AF: 0.362 AC: 3810 AN: 10528

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29675 AN: 67908

Other (OTH) AF: 0.454 AC: 960 AN: 2114

Alfa AF: 0.446 Hom.: 29899

Bravo AF: 0.457

Asia WGS AF: 0.604 AC: 2085 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs6968385; hg19: chr7-110047471;