rs1874226

chr17-39572778-C-T

Variant summary

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

The XR_934745.3(LOC105371770):n.203+150G>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 0.221 in 151,940 control chromosomes in the GnomAD database, including 4,379 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 0.22 (4379 hom., cov: 31)
• Consequence: LOC105371770 XR_934745.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

Genes affected

LOC105371770 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371770	XR_934745.3	n.203+150G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33539 AN: 151822 Hom.: 4378 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.221 AC: 33574 AN: 151940 Hom.: 4379 Cov.: 31 AF XY: 0.218 AC XY: 16171 AN XY: 74250

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.0821

Gnomad4 FIN AF: 0.0817

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.216

Alfa AF: 0.188 Hom.: 404

Bravo AF: 0.244

Asia WGS AF: 0.149 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.74
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1874226; hg19: chr17-37729031;