rs1835740

chr8-97154685-T-C

Variant summary

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

The NR_125390.1(LOC101927066):n.472-201075A>G 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 0.748 in 152,058 control chromosomes in the GnomAD database, including 42,938 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 0.75 (42938 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

LOC101927066 (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 (NFE) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927066	NR_125390.1	n.472-201075A>G		intron_variant, non_coding_transcript_variant
LOC105375655	XR_928434.3	n.174+4013T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113542 AN: 151942 Hom.: 42878 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.748 AC: 113670 AN: 152058 Hom.: 42938 Cov.: 32 AF XY: 0.745 AC XY: 55391 AN XY: 74348

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.731

Alfa AF: 0.760 Hom.: 92682

Bravo AF: 0.749

Asia WGS AF: 0.555 AC: 1930 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	1.6
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1835740; hg19: chr8-98166913; COSMIC: COSV70047773;