7-80339203-T-C

Variant names:

• chr7-80339203-T-C
• rs37935
• ENST00000598433.5:n.354-5436A>G

Variant summary

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

The ENST00000718128.1(ENSG00000232667):​n.365+22912A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 137,042 control chromosomes in the GnomAD database, including 20,863 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 0.54 (20863 hom., cov: 29)
• Consequence: ENSG00000232667 ENST00000718128.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 5 publications found

Genes affected

ENSG00000232667 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718128.1. 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
	ENSG00000232667	ENST00000598433.5	TSL:5	n.354-5436A>G		intron	N/A
	ENSG00000232667	ENST00000601205.5	TSL:5	n.381-276A>G		intron	N/A
	ENSG00000232667	ENST00000614372.5	TSL:5	n.1061-7835A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.543 AC: 74382 AN: 136918 Hom.: 20825 Cov.: 29

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.543 AC: 74473 AN: 137042 Hom.: 20863 Cov.: 29 AF XY: 0.545 AC XY: 36325 AN XY: 66690

African (AFR) AF: 0.794 AC: 32006 AN: 40328

American (AMR) AF: 0.429 AC: 5475 AN: 12768

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1492 AN: 3130

East Asian (EAS) AF: 0.378 AC: 1560 AN: 4132

South Asian (SAS) AF: 0.495 AC: 2295 AN: 4638

European-Finnish (FIN) AF: 0.458 AC: 4131 AN: 9016

Middle Eastern (MID) AF: 0.626 AC: 174 AN: 278

European-Non Finnish (NFE) AF: 0.434 AC: 26045 AN: 59966

Other (OTH) AF: 0.527 AC: 1011 AN: 1918

Alfa AF: 0.425 Hom.: 6470

Bravo AF: 0.499

Asia WGS AF: 0.411 AC: 1422 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.58
DANN	Benign	0.83
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs37935; hg19: chr7-79968519;