7-3089155-T-C

Variant names:

• chr7-3089155-T-C
• rs4722404
• ENST00000667422.1:n.76-1766A>G

Variant summary

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

The ENST00000667422.1(ENSG00000217455):​n.76-1766A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,004 control chromosomes in the GnomAD database, including 13,114 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 0.40 (13114 hom., cov: 32)
• Consequence: ENSG00000217455 ENST00000667422.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 34 publications found

Genes affected

ENSG00000217455 (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 (AMR) allele frequency at 95% confidence interval = 0.49 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
ENSG00000217455	ENST00000667422.1	n.76-1766A>G		intron_variant	Intron 1 of 1
ENSG00000217455	ENST00000716171.1	n.249-2735A>G		intron_variant	Intron 3 of 4
ENSG00000217455	ENST00000810303.1	n.186-2735A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61236 AN: 151886 Hom.: 13111 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.403 AC: 61257 AN: 152004 Hom.: 13114 Cov.: 32 AF XY: 0.405 AC XY: 30066 AN XY: 74276

African (AFR) AF: 0.262 AC: 10885 AN: 41480

American (AMR) AF: 0.500 AC: 7632 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1681 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1732 AN: 5144

South Asian (SAS) AF: 0.433 AC: 2086 AN: 4818

European-Finnish (FIN) AF: 0.466 AC: 4911 AN: 10536

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30713 AN: 67966

Other (OTH) AF: 0.444 AC: 937 AN: 2108

Alfa AF: 0.436 Hom.: 38753

Bravo AF: 0.401

Asia WGS AF: 0.361 AC: 1258 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	0.50
DANN	Benign	0.52
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs4722404; hg19: chr7-3128789;