chr7-110407907-C-T

Variant names:

• chr7-110407907-C-T
• rs4730430
• ENST00000658032.1:n.331-42617G>A

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.331-42617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,814 control chromosomes in the GnomAD database, including 13,718 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 0.42 (13718 hom., cov: 32)
• Consequence: ENSG00000226965 ENST00000658032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658032.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226965	ENST00000658032.1		n.331-42617G>A		intron	N/A
	ENSG00000226965	ENST00000666128.1		n.97+24904G>A		intron	N/A
	ENSG00000226965	ENST00000667232.1		n.411+24904G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63752 AN: 151696 Hom.: 13712 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.420 AC: 63787 AN: 151814 Hom.: 13718 Cov.: 32 AF XY: 0.419 AC XY: 31105 AN XY: 74168

African (AFR) AF: 0.456 AC: 18857 AN: 41396

American (AMR) AF: 0.421 AC: 6403 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1400 AN: 3470

East Asian (EAS) AF: 0.175 AC: 904 AN: 5162

South Asian (SAS) AF: 0.240 AC: 1153 AN: 4814

European-Finnish (FIN) AF: 0.545 AC: 5747 AN: 10552

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.412 AC: 28005 AN: 67908

Other (OTH) AF: 0.412 AC: 869 AN: 2108

Alfa AF: 0.403 Hom.: 27645

Bravo AF: 0.414

Asia WGS AF: 0.212 AC: 742 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.5
DANN	Benign	0.84
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs4730430; hg19: chr7-110047964;