rs2727338

Positions:

• chr17-63919006-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000647774.1(ENSG00000285947):​c.287-500T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 152,304 control chromosomes in the GnomAD database, including 52 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 0.024 (52 hom., cov: 33)
• Consequence: ENSG00000285947 ENST00000647774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521

Genes affected

ENSG00000285947 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0237 (3602/152304) while in subpopulation NFE AF= 0.0349 (2371/68010). AF 95% confidence interval is 0.0337. There are 52 homozygotes in gnomad4. There are 1735 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 52 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63919006A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285947	ENST00000647774.1	c.287-500T>C		intron_variant				ENSP00000497443.1

Frequencies

GnomAD3 genomes AF: 0.0236 AC: 3598 AN: 152186 Hom.: 51 Cov.: 33

Gnomad AFR AF: 0.00721

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0121

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.00911

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0237 AC: 3602 AN: 152304 Hom.: 52 Cov.: 33 AF XY: 0.0233 AC XY: 1735 AN XY: 74472

Gnomad4 AFR AF: 0.00729

Gnomad4 AMR AF: 0.0121

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.00911

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0349

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.0258 Hom.: 7

Bravo AF: 0.0206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2727338; hg19: chr17-61996366;