chr9-38746454-G-C

Variant names:

• chr9-38746454-G-C
• rs7042508
• ENST00000835853.1:n.185+18662G>C

Variant summary

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

The ENST00000835853.1(ENSG00000308694):​n.185+18662G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 152,026 control chromosomes in the GnomAD database, including 1,023 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 0.096 (1023 hom., cov: 33)
• Consequence: ENSG00000308694 ENST00000835853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 2 publications found

Genes affected

ENSG00000308694 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835853.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308694	ENST00000835853.1		n.185+18662G>C		intron	N/A
	ENSG00000308694	ENST00000835854.1		n.376+8246G>C		intron	N/A
	ENSG00000308694	ENST00000835855.1		n.72+18662G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14542 AN: 151906 Hom.: 1019 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0422

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0815

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

GnomAD4 genome AF: 0.0958 AC: 14568 AN: 152026 Hom.: 1023 Cov.: 33 AF XY: 0.0926 AC XY: 6884 AN XY: 74340

African (AFR) AF: 0.191 AC: 7893 AN: 41300

American (AMR) AF: 0.0560 AC: 857 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3470

East Asian (EAS) AF: 0.102 AC: 529 AN: 5180

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4824

European-Finnish (FIN) AF: 0.0422 AC: 448 AN: 10616

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0622 AC: 4233 AN: 68022

Other (OTH) AF: 0.0797 AC: 168 AN: 2108

Alfa AF: 0.0768 Hom.: 72

Bravo AF: 0.104

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs7042508; hg19: chr9-38746451;