rs140837

Variant names:

• chr6-3708672-ACT-A
• rs140837
• ENST00000653557.1:n.715+10689_715+10690delAG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NR_187641.1(LOC100507336):​n.609+10689_609+10690delAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,904 control chromosomes in the GnomAD database, including 5,410 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5410 hom., cov: 24)
• Consequence: LOC100507336 NR_187641.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 2 publications found

Genes affected

ENSG00000228793 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187641.1. 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
	LOC100507336	NR_187641.1		n.609+10689_609+10690delAG		intron	N/A
	LOC100507336	NR_187642.1		n.715+10689_715+10690delAG		intron	N/A
	LOC100507336	NR_187643.1		n.715+10689_715+10690delAG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228793	ENST00000653557.1		n.715+10689_715+10690delAG		intron	N/A
	ENSG00000228793	ENST00000653626.1		n.458+10689_458+10690delAG		intron	N/A
	ENSG00000228793	ENST00000655328.1		n.715+10689_715+10690delAG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38437 AN: 151786 Hom.: 5409 Cov.: 24

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.253 AC: 38461 AN: 151904 Hom.: 5410 Cov.: 24 AF XY: 0.254 AC XY: 18890 AN XY: 74256

African (AFR) AF: 0.359 AC: 14853 AN: 41394

American (AMR) AF: 0.225 AC: 3440 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3468

East Asian (EAS) AF: 0.479 AC: 2465 AN: 5142

South Asian (SAS) AF: 0.131 AC: 633 AN: 4822

European-Finnish (FIN) AF: 0.261 AC: 2752 AN: 10562

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

European-Non Finnish (NFE) AF: 0.194 AC: 13147 AN: 67926

Other (OTH) AF: 0.230 AC: 486 AN: 2110

Alfa AF: 0.224 Hom.: 495

Bravo AF: 0.259

Asia WGS AF: 0.272 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs140837; hg19: chr6-3708906;