ENST00000439694.6:n.655+8910A>G

Variant names:

• chr7-137022995-T-C
• rs324654
• ENST00000439694.6:n.655+8910A>G

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.655+8910A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,066 control chromosomes in the GnomAD database, including 67,919 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 0.94 (67919 hom., cov: 33)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 1 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC349160	NR_046103.1	n.341+9799A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234352	ENST00000439694.6	n.655+8910A>G		intron_variant	Intron 3 of 3	1
ENSG00000234352	ENST00000425981.2	n.341+9799A>G		intron_variant	Intron 2 of 3	2
ENSG00000234352	ENST00000586239.5	n.273+9799A>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143387 AN: 151948 Hom.: 67865 Cov.: 33

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.944 AC: 143497 AN: 152066 Hom.: 67919 Cov.: 33 AF XY: 0.942 AC XY: 70048 AN XY: 74330

African (AFR) AF: 0.987 AC: 41026 AN: 41558

American (AMR) AF: 0.936 AC: 14265 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3353 AN: 3468

East Asian (EAS) AF: 0.742 AC: 3796 AN: 5118

South Asian (SAS) AF: 0.816 AC: 3932 AN: 4820

European-Finnish (FIN) AF: 0.967 AC: 10274 AN: 10626

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.938 AC: 63705 AN: 67908

Other (OTH) AF: 0.939 AC: 1986 AN: 2114

Alfa AF: 0.941 Hom.: 76434

Bravo AF: 0.943

Asia WGS AF: 0.826 AC: 2871 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs324654; hg19: chr7-136707742;