17-71735940-G-T

Position:

• chr17-71735940-G-T

Variant summary

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

The ENST00000670823.1(ENSG00000286387):​n.45+7484C>A 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 0.187 in 152,078 control chromosomes in the GnomAD database, including 7,054 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 0.19 (7054 hom., cov: 32)
• Consequence: ENST00000670823.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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
	ENST00000670823.1	n.45+7484C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28330 AN: 151960 Hom.: 7019 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.187 AC: 28429 AN: 152078 Hom.: 7054 Cov.: 32 AF XY: 0.186 AC XY: 13802 AN XY: 74334

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.0397

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0544

Gnomad4 NFE AF: 0.0194

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0174 Hom.: 30

Bravo AF: 0.206

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	13
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2253624; hg19: chr17-69732081;