17-37662786-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000615265.1(ENSG00000277501):n.590+19250A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,122 control chromosomes in the GnomAD database, including 11,483 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 0.35 (11483 hom., cov: 32)
• Consequence: ENST00000615265.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000615265.1	n.590+19250A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000613901.1	n.109-13038A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53678 AN: 152004 Hom.: 11447 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.354 AC: 53784 AN: 152122 Hom.: 11483 Cov.: 32 AF XY: 0.350 AC XY: 26005 AN XY: 74384

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.335

Alfa AF: 0.261 Hom.: 11256

Bravo AF: 0.391

Asia WGS AF: 0.280 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.5
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4074770; hg19: chr17-36022817;