rs562106

chr6-95971274-A-Cchr6-95971274-A-Gchr6-95971274-A-T

Variant summary

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

The ENST00000668456.1(ENSG00000287578):n.105+44013T>G 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 0.141 in 151,558 control chromosomes in the GnomAD database, including 1,722 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 0.14 (1722 hom., cov: 30)
• Consequence: ENST00000668456.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986626	XR_001744263.2	n.147+44013T>G		intron_variant, non_coding_transcript_variant
LOC107986626	XR_001744264.2	n.147+44013T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668456.1	n.105+44013T>G		intron_variant, non_coding_transcript_variant
	ENST00000658251.1	n.75+43653T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21359 AN: 151446 Hom.: 1718 Cov.: 30

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.00545

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0674

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.141 AC: 21388 AN: 151558 Hom.: 1722 Cov.: 30 AF XY: 0.140 AC XY: 10388 AN XY: 74082

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.00546

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0674

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0536 Hom.: 61

Bravo AF: 0.149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.62
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs562106; hg19: chr6-96419150;