rs140837

chr6-3708672-ACT-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000665760.1(ENSG00000228793):n.715+10689_715+10690del 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 0.253 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: ENST00000665760.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507336	XR_001743929.2	n.715+10689_715+10690del		intron_variant, non_coding_transcript_variant
LOC100507336	XR_926401.3	n.715+10689_715+10690del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665760.1	n.715+10689_715+10690del		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.230

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 v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs140837; hg19: chr6-3708906;