rs37936

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000232667 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232667	ENST00000598433.5	n.354-5975T>C		intron_variant	Intron 3 of 6	5
ENSG00000232667	ENST00000601205.5	n.381-815T>C		intron_variant	Intron 3 of 3	5
ENSG00000232667	ENST00000626415.1	n.24-9215T>C		intron_variant	Intron 1 of 1	5

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

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.480

Alfa AF: 0.425 Hom.: 6309

Bravo AF: 0.500

Asia WGS AF: 0.412 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.9
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs37936; hg19: chr7-79969058;