rs1330106

Positions:

• chr6-119844329-G-A
• chr6-119844329-G-T

Variant summary

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

The NR_134600.1(LOC105377975):​n.295-238G>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 0.215 in 152,092 control chromosomes in the GnomAD database, including 3,950 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 (3950 hom., cov: 32)
• Consequence: LOC105377975 NR_134600.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

Genes affected

LOC105377975 (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 = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377975	NR_134600.1	n.295-238G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32727 AN: 151974 Hom.: 3948 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.215 AC: 32734 AN: 152092 Hom.: 3950 Cov.: 32 AF XY: 0.220 AC XY: 16347 AN XY: 74344

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.220

Alfa AF: 0.232 Hom.: 6668

Bravo AF: 0.206

Asia WGS AF: 0.257 AC: 894 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	3.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330106; hg19: chr6-120165475;