7-110134214-C-T

Variant names:

• chr7-110134214-C-T
• rs1722047
• ENST00000658032.1:n.439-23513G>A

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.439-23513G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 151,440 control chromosomes in the GnomAD database, including 38,473 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 0.71 (38473 hom., cov: 30)
• Consequence: ENSG00000226965 ENST00000658032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.766 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.439-23513G>A		intron_variant	Intron 5 of 5
ENSG00000226965	ENST00000667232.1	n.520-23513G>A		intron_variant	Intron 6 of 7
ENSG00000226965	ENST00000755897.1	n.34-25884G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107544 AN: 151322 Hom.: 38437 Cov.: 30

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.711 AC: 107635 AN: 151440 Hom.: 38473 Cov.: 30 AF XY: 0.709 AC XY: 52468 AN XY: 74010

African (AFR) AF: 0.772 AC: 31947 AN: 41366

American (AMR) AF: 0.670 AC: 10163 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1970 AN: 3462

East Asian (EAS) AF: 0.786 AC: 4022 AN: 5118

South Asian (SAS) AF: 0.783 AC: 3762 AN: 4806

European-Finnish (FIN) AF: 0.639 AC: 6732 AN: 10536

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 46964 AN: 67686

Other (OTH) AF: 0.674 AC: 1411 AN: 2094

Alfa AF: 0.696 Hom.: 152137

Bravo AF: 0.712

Asia WGS AF: 0.761 AC: 2642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1722047; hg19: chr7-109774271;