rs75316749

Positions:

• chr3-169043635-A-G

Variant summary

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

The XR_001740574.2(LOC107986051):​n.80-11827T>C 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 0.0431 in 152,262 control chromosomes in the GnomAD database, including 158 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 0.043 (158 hom., cov: 32)
• Consequence: LOC107986051 XR_001740574.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

Genes affected

LOC107986051 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986051	XR_001740574.2	n.80-11827T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0431 AC: 6562 AN: 152144 Hom.: 158 Cov.: 32

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.00868

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0431 AC: 6559 AN: 152262 Hom.: 158 Cov.: 32 AF XY: 0.0424 AC XY: 3155 AN XY: 74452

Gnomad4 AFR AF: 0.0427

Gnomad4 AMR AF: 0.0385

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.0405

Gnomad4 SAS AF: 0.0861

Gnomad4 FIN AF: 0.00868

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0413 Hom.: 24

Bravo AF: 0.0454

Asia WGS AF: 0.0530 AC: 184 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.060
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75316749; hg19: chr3-168761423;