7-110228018-G-T

Variant names:

• chr7-110228018-G-T
• rs1013920
• ENST00000658032.1:n.406-47008C>A

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.406-47008C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,908 control chromosomes in the GnomAD database, including 28,636 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 0.61 (28636 hom., cov: 32)
• Consequence: ENSG00000226965 ENST00000658032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226965	ENST00000658032.1	n.406-47008C>A		intron_variant	Intron 4 of 5
ENSG00000226965	ENST00000667232.1	n.487-47008C>A		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92563 AN: 151790 Hom.: 28606 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.610 AC: 92643 AN: 151908 Hom.: 28636 Cov.: 32 AF XY: 0.616 AC XY: 45750 AN XY: 74222

African (AFR) AF: 0.725 AC: 30086 AN: 41470

American (AMR) AF: 0.598 AC: 9135 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1806 AN: 3468

East Asian (EAS) AF: 0.605 AC: 3119 AN: 5154

South Asian (SAS) AF: 0.696 AC: 3360 AN: 4826

European-Finnish (FIN) AF: 0.560 AC: 5887 AN: 10520

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.546 AC: 37060 AN: 67878

Other (OTH) AF: 0.611 AC: 1290 AN: 2110

Alfa AF: 0.466 Hom.: 1341

Bravo AF: 0.614

Asia WGS AF: 0.649 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.61
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1013920; hg19: chr7-109868075; COSMIC: COSV107155413;