rs180156

Positions:

• chr17-70025996-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000435112.5(ENSG00000230258):​n.307-3799C>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 0.828 in 152,192 control chromosomes in the GnomAD database, including 52,251 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 0.83 (52251 hom., cov: 33)
• Consequence: ENST00000435112.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112267896	XR_001752989.3	n.88-3799C>A		intron_variant, non_coding_transcript_variant
LOC105371881	XR_934952.3	n.1583-29159C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435112.5	n.307-3799C>A		intron_variant, non_coding_transcript_variant		3
	ENST00000587325.1	n.319-3799C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125955 AN: 152074 Hom.: 52224 Cov.: 33

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.828 AC: 126029 AN: 152192 Hom.: 52251 Cov.: 33 AF XY: 0.831 AC XY: 61871 AN XY: 74422

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.810

Alfa AF: 0.836 Hom.: 6623

Bravo AF: 0.818

Asia WGS AF: 0.848 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	9.0
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180156; hg19: chr17-68022137;