chr6-105881180-C-T

Variant names:

• chr6-105881180-C-T
• rs9386485
• ENST00000642235.1:n.144+3846G>A

Variant summary

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

The ENST00000642235.1(ENSG00000284999):​n.144+3846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,970 control chromosomes in the GnomAD database, including 19,366 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 0.50 (19366 hom., cov: 32)
• Consequence: ENSG00000284999 ENST00000642235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 6 publications found

Genes affected

ENSG00000284999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377923	XR_001744274.2	n.296+3846G>A		intron_variant	Intron 2 of 2
LOC105377923	XR_001744275.2	n.200+3846G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284999	ENST00000642235.1	n.144+3846G>A		intron_variant	Intron 2 of 2
ENSG00000284999	ENST00000644129.1	n.144+3846G>A		intron_variant	Intron 2 of 3
ENSG00000284999	ENST00000744159.1	n.237+3846G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76147 AN: 151850 Hom.: 19331 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.502 AC: 76234 AN: 151970 Hom.: 19366 Cov.: 32 AF XY: 0.501 AC XY: 37230 AN XY: 74242

African (AFR) AF: 0.578 AC: 23950 AN: 41450

American (AMR) AF: 0.432 AC: 6600 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1807 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2430 AN: 5178

South Asian (SAS) AF: 0.427 AC: 2053 AN: 4804

European-Finnish (FIN) AF: 0.510 AC: 5366 AN: 10518

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32354 AN: 67962

Other (OTH) AF: 0.479 AC: 1012 AN: 2112

Alfa AF: 0.476 Hom.: 24977

Bravo AF: 0.497

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs9386485; hg19: chr6-106329055;