rs196458

Positions:

• chr6-168717241-G-T

Variant summary

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

The XR_943296.3(LOC105378143):​n.6748G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.932 in 151,856 control chromosomes in the GnomAD database, including 65,989 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 0.93 (65989 hom., cov: 29)
• Consequence: LOC105378143 XR_943296.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

Genes affected

LOC105378143 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=1.857).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378143	XR_943296.3	n.6748G>T		non_coding_transcript_exon_variant	3/3
LOC105378143	XR_001744472.2	n.6478G>T		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000436492.1	n.80+556G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141411 AN: 151738 Hom.: 65947 Cov.: 29

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.932 AC: 141513 AN: 151856 Hom.: 65989 Cov.: 29 AF XY: 0.931 AC XY: 69075 AN XY: 74172

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.920

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.939

Alfa AF: 0.924 Hom.: 8054

Bravo AF: 0.934

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs196458; hg19: -;