chr7-97026414-T-C

Variant names:

• chr7-97026414-T-C
• rs1207735
• ENST00000737842.1:n.18A>G

Variant summary

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

The ENST00000737842.1(ENSG00000296293):​n.18A>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 0.734 in 152,106 control chromosomes in the GnomAD database, including 41,494 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 0.73 (41494 hom., cov: 31)
• Consequence: ENSG00000296293 ENST00000737842.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504
• Publications: 3 publications found

Genes affected

ENSG00000296293 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737842.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296293	ENST00000737842.1		n.18A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000296253	ENST00000737642.1		n.110-1043T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111533 AN: 151988 Hom.: 41443 Cov.: 31

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.734 AC: 111643 AN: 152106 Hom.: 41494 Cov.: 31 AF XY: 0.730 AC XY: 54272 AN XY: 74338

African (AFR) AF: 0.854 AC: 35425 AN: 41482

American (AMR) AF: 0.628 AC: 9597 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2314 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4009 AN: 5172

South Asian (SAS) AF: 0.677 AC: 3258 AN: 4814

European-Finnish (FIN) AF: 0.689 AC: 7292 AN: 10576

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47457 AN: 67984

Other (OTH) AF: 0.714 AC: 1505 AN: 2108

Alfa AF: 0.741 Hom.: 5966

Bravo AF: 0.733

Asia WGS AF: 0.717 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.27
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1207735; hg19: chr7-96655726;