chr6-153359137-A-T

Variant names:

• chr6-153359137-A-T
• rs1768996
• ENST00000436953.2:n.387-7401T>A

Variant summary

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

The ENST00000436953.2(ENSG00000237312):​n.387-7401T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 150,096 control chromosomes in the GnomAD database, including 31,319 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 0.65 (31319 hom., cov: 29)
• Consequence: ENSG00000237312 ENST00000436953.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657
• Publications: 2 publications found

Genes affected

ENSG00000237312 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436953.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105378066	NR_187983.1		n.397-7401T>A		intron	N/A
	LOC105378066	NR_187984.1		n.397-7401T>A		intron	N/A
	LOC105378066	NR_187985.1		n.397-7401T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237312	ENST00000436953.2	TSL:3	n.387-7401T>A		intron	N/A
	ENSG00000237312	ENST00000836504.1		n.355-7401T>A		intron	N/A
	ENSG00000237312	ENST00000836505.1		n.276-34877T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.645 AC: 96772 AN: 150020 Hom.: 31304 Cov.: 29

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.645 AC: 96819 AN: 150096 Hom.: 31319 Cov.: 29 AF XY: 0.648 AC XY: 47438 AN XY: 73152

African (AFR) AF: 0.679 AC: 27764 AN: 40866

American (AMR) AF: 0.539 AC: 8125 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2306 AN: 3454

East Asian (EAS) AF: 0.736 AC: 3743 AN: 5088

South Asian (SAS) AF: 0.698 AC: 3339 AN: 4782

European-Finnish (FIN) AF: 0.684 AC: 6802 AN: 9950

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42622 AN: 67586

Other (OTH) AF: 0.636 AC: 1333 AN: 2096

Alfa AF: 0.629 Hom.: 3488

Bravo AF: 0.632

Asia WGS AF: 0.672 AC: 2312 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.0
DANN	Benign	0.57
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1768996; hg19: chr6-153680272;