rs2029870

Positions:

• chr6-164467333-G-A
• chr6-164467333-G-T

Variant summary

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

The XR_001744460.3(LOC107986667):​n.249+29511G>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 0.223 in 151,612 control chromosomes in the GnomAD database, including 4,035 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 (4035 hom., cov: 31)
• Consequence: LOC107986667 XR_001744460.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

Genes affected

LOC107986667 (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 (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986667	XR_001744460.3	n.249+29511G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33815 AN: 151496 Hom.: 4025 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.223 AC: 33862 AN: 151612 Hom.: 4035 Cov.: 31 AF XY: 0.225 AC XY: 16650 AN XY: 74064

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.217

Alfa AF: 0.201 Hom.: 6659

Bravo AF: 0.235

Asia WGS AF: 0.361 AC: 1254 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	3.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2029870; hg19: chr6-164888366;