rs6912842

Variant names:

• chr6-18055159-G-T
• rs6912842
• ENST00000747204.1:n.89-526G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000747204.1(ENSG00000297344):​n.89-526G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,080 control chromosomes in the GnomAD database, including 1,051 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 0.11 (1051 hom., cov: 32)
• Consequence: ENSG00000297344 ENST00000747204.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.642
• Publications: 2 publications found

Genes affected

ENSG00000297344 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297344	ENST00000747204.1	n.89-526G>T		intron_variant	Intron 1 of 3
ENSG00000297344	ENST00000747205.1	n.179-526G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16805 AN: 151962 Hom.: 1051 Cov.: 32

Gnomad AFR AF: 0.0571

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.110 AC: 16799 AN: 152080 Hom.: 1051 Cov.: 32 AF XY: 0.109 AC XY: 8130 AN XY: 74342

African (AFR) AF: 0.0571 AC: 2368 AN: 41484

American (AMR) AF: 0.0923 AC: 1410 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5168

South Asian (SAS) AF: 0.114 AC: 547 AN: 4808

European-Finnish (FIN) AF: 0.127 AC: 1341 AN: 10572

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.148 AC: 10089 AN: 67986

Other (OTH) AF: 0.114 AC: 241 AN: 2112

Alfa AF: 0.124 Hom.: 199

Bravo AF: 0.104

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.45
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs6912842; hg19: chr6-18055390;