17-40890629-C-A

Position:

• chr17-40890629-C-A

Variant summary

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

The XR_934754.3(LOC105371777):​n.64-27600C>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 0.673 in 152,012 control chromosomes in the GnomAD database, including 35,822 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 0.67 (35822 hom., cov: 32)
• Consequence: LOC105371777 XR_934754.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

LOC105371777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371777	XR_934754.3	n.64-27600C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102136 AN: 151896 Hom.: 35774 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.673 AC: 102234 AN: 152012 Hom.: 35822 Cov.: 32 AF XY: 0.680 AC XY: 50520 AN XY: 74296

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.624

Alfa AF: 0.573 Hom.: 47844

Bravo AF: 0.681

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.057
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2315504; hg19: chr17-39046881;