7-136862169-C-T

Variant names:

• chr7-136862169-C-T
• rs6467694
• ENST00000439694.6:n.656-76278G>A

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.656-76278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 152,232 control chromosomes in the GnomAD database, including 56,354 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 0.86 (56354 hom., cov: 33)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234352	ENST00000439694.6	n.656-76278G>A		intron_variant	Intron 3 of 3	1
ENSG00000234352	ENST00000586239.5	n.274-76278G>A		intron_variant	Intron 2 of 4	5
ENSG00000234352	ENST00000592183.5	n.475-76278G>A		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130491 AN: 152114 Hom.: 56304 Cov.: 33

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.858 AC: 130599 AN: 152232 Hom.: 56354 Cov.: 33 AF XY: 0.858 AC XY: 63856 AN XY: 74428

African (AFR) AF: 0.781 AC: 32402 AN: 41508

American (AMR) AF: 0.876 AC: 13387 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3106 AN: 3470

East Asian (EAS) AF: 0.835 AC: 4325 AN: 5178

South Asian (SAS) AF: 0.712 AC: 3435 AN: 4822

European-Finnish (FIN) AF: 0.936 AC: 9935 AN: 10614

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61111 AN: 68038

Other (OTH) AF: 0.882 AC: 1858 AN: 2106

Alfa AF: 0.882 Hom.: 201482

Bravo AF: 0.851

Asia WGS AF: 0.781 AC: 2716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.047
DANN	Benign	0.44
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6467694; hg19: chr7-136546916;