rs16970570

chr17-77826765-G-A

Variant summary

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

The XR_935001.2(LOC105371908):n.155+13719C>T 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 0.135 in 151,952 control chromosomes in the GnomAD database, including 2,172 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 0.13 (2172 hom., cov: 32)
• Consequence: LOC105371908 XR_935001.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

Genes affected

LOC105371908 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371908	XR_935001.2	n.155+13719C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20418 AN: 151834 Hom.: 2165 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.135 AC: 20453 AN: 151952 Hom.: 2172 Cov.: 32 AF XY: 0.135 AC XY: 9997 AN XY: 74282

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.0790

Gnomad4 ASJ AF: 0.0701

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.0946

Gnomad4 FIN AF: 0.0665

Gnomad4 NFE AF: 0.0658

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0754 Hom.: 825

Bravo AF: 0.144

Asia WGS AF: 0.153 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.67
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16970570; hg19: chr17-75822847;