chr7-110241718-C-T

Variant names:

• chr7-110241718-C-T
• rs17157509
• ENST00000658032.1:n.406-60708G>A

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.406-60708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,942 control chromosomes in the GnomAD database, including 5,789 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 0.25 (5789 hom., cov: 31)
• Consequence: ENSG00000226965 ENST00000658032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 1 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 = 0.529 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226965	ENST00000658032.1		n.406-60708G>A		intron	N/A
	ENSG00000226965	ENST00000667232.1		n.487-60708G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38362 AN: 151824 Hom.: 5790 Cov.: 31

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.252 AC: 38362 AN: 151942 Hom.: 5789 Cov.: 31 AF XY: 0.257 AC XY: 19045 AN XY: 74228

African (AFR) AF: 0.0953 AC: 3951 AN: 41442

American (AMR) AF: 0.344 AC: 5245 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 942 AN: 3468

East Asian (EAS) AF: 0.546 AC: 2825 AN: 5174

South Asian (SAS) AF: 0.256 AC: 1230 AN: 4808

European-Finnish (FIN) AF: 0.253 AC: 2661 AN: 10522

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20526 AN: 67956

Other (OTH) AF: 0.274 AC: 578 AN: 2112

Alfa AF: 0.255 Hom.: 2544

Bravo AF: 0.252

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.24
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs17157509; hg19: chr7-109881775;