rs7667506

Variant names:

• chr4-66735249-G-A
• rs7667506
• ENST00000840785.1:n.387C>T

Variant summary

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

The ENST00000840785.1(ENSG00000309403):​n.387C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.953 in 152,330 control chromosomes in the GnomAD database, including 69,212 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 0.95 (69212 hom., cov: 33)
• Consequence: ENSG00000309403 ENST00000840785.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 1 publications found

Genes affected

ENSG00000309403 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 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
ENSG00000309403	ENST00000840785.1	n.387C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.953 AC: 145034 AN: 152212 Hom.: 69168 Cov.: 33

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.953 AC: 145134 AN: 152330 Hom.: 69212 Cov.: 33 AF XY: 0.952 AC XY: 70918 AN XY: 74480

African (AFR) AF: 0.909 AC: 37769 AN: 41572

American (AMR) AF: 0.969 AC: 14813 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3306 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4973 AN: 5176

South Asian (SAS) AF: 0.952 AC: 4600 AN: 4832

European-Finnish (FIN) AF: 0.967 AC: 10272 AN: 10620

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66229 AN: 68044

Other (OTH) AF: 0.934 AC: 1977 AN: 2116

Alfa AF: 0.965 Hom.: 14373

Bravo AF: 0.950

Asia WGS AF: 0.933 AC: 3246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.078
DANN	Benign	0.66
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7667506; hg19: chr4-67600967;