7-155968169-T-G

Variant names:

• chr7-155968169-T-G
• rs2363910
• ENST00000683260.1:n.4050T>G

Variant summary

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

The ENST00000683260.1(ENSG00000204876):​n.4050T>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 0.877 in 152,122 control chromosomes in the GnomAD database, including 58,696 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 0.88 (58696 hom., cov: 32)
• Consequence: ENSG00000204876 ENST00000683260.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 5 publications found

Genes affected

ENSG00000204876 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000683260.1. 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
	LOC389602	NR_144629.2		n.3928T>G		non_coding_transcript_exon	Exon 2 of 2
	LOC389602	NR_168378.1		n.4437T>G		non_coding_transcript_exon	Exon 2 of 2
	LOC389602	NR_168379.1		n.4211T>G		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000204876	ENST00000683260.1		n.4050T>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133355 AN: 152004 Hom.: 58679 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.877 AC: 133423 AN: 152122 Hom.: 58696 Cov.: 32 AF XY: 0.874 AC XY: 65004 AN XY: 74366

African (AFR) AF: 0.857 AC: 35527 AN: 41448

American (AMR) AF: 0.842 AC: 12876 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3229 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3650 AN: 5182

South Asian (SAS) AF: 0.859 AC: 4139 AN: 4820

European-Finnish (FIN) AF: 0.873 AC: 9252 AN: 10600

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61734 AN: 68000

Other (OTH) AF: 0.877 AC: 1846 AN: 2106

Alfa AF: 0.870 Hom.: 5807

Bravo AF: 0.870

Asia WGS AF: 0.753 AC: 2623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2363910; hg19: chr7-155760863;