chr7-109873860-G-A

Variant names:

• chr7-109873860-G-A
• rs10953645
• ENST00000830489.1:n.73+26506C>T

Variant summary

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

The ENST00000830489.1(ENSG00000308019):​n.73+26506C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,884 control chromosomes in the GnomAD database, including 10,573 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 0.36 (10573 hom., cov: 32)
• Consequence: ENSG00000308019 ENST00000830489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 3 publications found

Genes affected

ENSG00000308019 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830489.1. 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
	ENSG00000308019	ENST00000830489.1		n.73+26506C>T		intron	N/A
	ENSG00000308019	ENST00000830490.1		n.61+26506C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54374 AN: 151766 Hom.: 10575 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.358 AC: 54391 AN: 151884 Hom.: 10573 Cov.: 32 AF XY: 0.357 AC XY: 26488 AN XY: 74242

African (AFR) AF: 0.218 AC: 9038 AN: 41420

American (AMR) AF: 0.306 AC: 4672 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1646 AN: 3464

East Asian (EAS) AF: 0.313 AC: 1612 AN: 5158

South Asian (SAS) AF: 0.421 AC: 2030 AN: 4818

European-Finnish (FIN) AF: 0.400 AC: 4211 AN: 10516

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29832 AN: 67930

Other (OTH) AF: 0.391 AC: 826 AN: 2110

Alfa AF: 0.409 Hom.: 24651

Bravo AF: 0.340

Asia WGS AF: 0.362 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10953645; hg19: chr7-109513917;