rs7667261

Variant names:

• chr4-99090149-C-G
• rs7667261
• ENST00000500358.6:n.428+865C>G

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.428+865C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 152,222 control chromosomes in the GnomAD database, including 754 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 0.077 (754 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 3 publications found

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500358.6. 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
	LOC100507053	NR_037884.1		n.428+865C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246090	ENST00000500358.6	TSL:1	n.428+865C>G		intron	N/A
	ENSG00000246090	ENST00000757875.1		n.712C>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000246090	ENST00000499178.3	TSL:3	n.415+865C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11723 AN: 152104 Hom.: 752 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0401

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0389

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0772 AC: 11747 AN: 152222 Hom.: 754 Cov.: 32 AF XY: 0.0756 AC XY: 5625 AN XY: 74444

African (AFR) AF: 0.187 AC: 7737 AN: 41472

American (AMR) AF: 0.0401 AC: 613 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0143 AC: 69 AN: 4822

European-Finnish (FIN) AF: 0.0416 AC: 442 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0389 AC: 2645 AN: 68032

Other (OTH) AF: 0.0619 AC: 131 AN: 2116

Alfa AF: 0.0608 Hom.: 63

Bravo AF: 0.0821

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7667261; hg19: chr4-100011300;