7-155217003-T-G

Variant names:

• chr7-155217003-T-G
• rs1561176
• ENST00000663395.2:n.1689T>G

Variant summary

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

The ENST00000663395.2(ENSG00000228521):​n.1689T>G 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 0.158 in 151,934 control chromosomes in the GnomAD database, including 2,248 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 0.16 (2248 hom., cov: 32)
• Consequence: ENSG00000228521 ENST00000663395.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 5 publications found

Genes affected

ENSG00000228521 (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 (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663395.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228521	ENST00000663395.2		n.1689T>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000228521	ENST00000756834.1		n.1065T>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000228521	ENST00000756810.1		n.134+2726T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24001 AN: 151816 Hom.: 2248 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.158 AC: 24018 AN: 151934 Hom.: 2248 Cov.: 32 AF XY: 0.166 AC XY: 12314 AN XY: 74220

African (AFR) AF: 0.100 AC: 4155 AN: 41464

American (AMR) AF: 0.203 AC: 3101 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2273 AN: 5134

South Asian (SAS) AF: 0.220 AC: 1057 AN: 4812

European-Finnish (FIN) AF: 0.220 AC: 2317 AN: 10518

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10075 AN: 67972

Other (OTH) AF: 0.150 AC: 317 AN: 2114

Alfa AF: 0.105 Hom.: 251

Bravo AF: 0.153

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.74
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs1561176; hg19: chr7-155008713;