6-153338861-T-C

Variant names:

• chr6-153338861-T-C
• rs2503791
• ENST00000392385.2:n.170-7585T>C

Variant summary

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

The ENST00000392385.2(ENSG00000213121):​n.170-7585T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,718 control chromosomes in the GnomAD database, including 25,613 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 0.57 (25613 hom., cov: 31)
• Consequence: ENSG00000213121 ENST00000392385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 1 publications found

Genes affected

ENSG00000213121 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000392385.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105378066	NR_187983.1		n.476+12796A>G		intron	N/A
	LOC105378066	NR_187984.1		n.476+12796A>G		intron	N/A
	LOC105378066	NR_187985.1		n.476+12796A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000213121	ENST00000392385.2	TSL:2	n.170-7585T>C		intron	N/A
	ENSG00000237312	ENST00000436953.2	TSL:3	n.466+12796A>G		intron	N/A
	ENSG00000237312	ENST00000836504.1		n.434+12796A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86810 AN: 151604 Hom.: 25572 Cov.: 31

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.573 AC: 86898 AN: 151718 Hom.: 25613 Cov.: 31 AF XY: 0.576 AC XY: 42697 AN XY: 74110

African (AFR) AF: 0.694 AC: 28730 AN: 41390

American (AMR) AF: 0.605 AC: 9208 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3466

East Asian (EAS) AF: 0.622 AC: 3203 AN: 5152

South Asian (SAS) AF: 0.585 AC: 2812 AN: 4810

European-Finnish (FIN) AF: 0.557 AC: 5863 AN: 10532

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.496 AC: 33662 AN: 67836

Other (OTH) AF: 0.537 AC: 1133 AN: 2108

Alfa AF: 0.536 Hom.: 2763

Bravo AF: 0.580

Asia WGS AF: 0.593 AC: 2058 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.53
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2503791; hg19: chr6-153659996;