rs951251

Positions:

• chr6-131070072-G-A

Variant summary

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

The XR_942993.3(LOC105378004):​n.331+1062G>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 0.148 in 152,114 control chromosomes in the GnomAD database, including 2,308 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 0.15 (2308 hom., cov: 32)
• Consequence: LOC105378004 XR_942993.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

LOC105378004 (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 (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378004	XR_942993.3	n.331+1062G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22553 AN: 151996 Hom.: 2302 Cov.: 32

Gnomad AFR AF: 0.0367

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.148 AC: 22572 AN: 152114 Hom.: 2308 Cov.: 32 AF XY: 0.154 AC XY: 11454 AN XY: 74342

Gnomad4 AFR AF: 0.0367

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.146

Alfa AF: 0.165 Hom.: 1043

Bravo AF: 0.137

Asia WGS AF: 0.313 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.97
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951251; hg19: chr6-131391212;