7-80339742-A-G

Variant names:

• chr7-80339742-A-G
• rs37936
• ENST00000598433.5:n.354-5975T>C

Variant summary

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

The ENST00000598433.5(ENSG00000232667):​n.354-5975T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,062 control chromosomes in the GnomAD database, including 21,065 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 0.49 (21065 hom., cov: 32)
• Consequence: ENSG00000232667 ENST00000598433.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 6 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598433.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232667	ENST00000598433.5	TSL:5	n.354-5975T>C		intron	N/A
	ENSG00000232667	ENST00000601205.5	TSL:5	n.381-815T>C		intron	N/A
	ENSG00000232667	ENST00000614372.5	TSL:5	n.1061-8374T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74786 AN: 151944 Hom.: 21026 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.492 AC: 74877 AN: 152062 Hom.: 21065 Cov.: 32 AF XY: 0.492 AC XY: 36542 AN XY: 74340

African (AFR) AF: 0.779 AC: 32309 AN: 41486

American (AMR) AF: 0.361 AC: 5514 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1500 AN: 3466

East Asian (EAS) AF: 0.292 AC: 1509 AN: 5176

South Asian (SAS) AF: 0.480 AC: 2315 AN: 4826

European-Finnish (FIN) AF: 0.397 AC: 4190 AN: 10556

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26067 AN: 67956

Other (OTH) AF: 0.480 AC: 1015 AN: 2114

Alfa AF: 0.427 Hom.: 7200

Bravo AF: 0.500

Asia WGS AF: 0.412 AC: 1436 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	3.9
DANN	Benign	0.82
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs37936; hg19: chr7-79969058;