chr6-83502217-C-T

Variant names:

• chr6-83502217-C-T
• rs10943944
• ENST00000738470.1:n.36+10548G>A

Variant summary

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

The ENST00000738470.1(ENSG00000296350):​n.36+10548G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,918 control chromosomes in the GnomAD database, including 5,382 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 0.24 (5382 hom., cov: 31)
• Consequence: ENSG00000296350 ENST00000738470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 3 publications found

Genes affected

ENSG00000296350 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296350	ENST00000738470.1	n.36+10548G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36344 AN: 151798 Hom.: 5373 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.240 AC: 36400 AN: 151918 Hom.: 5382 Cov.: 31 AF XY: 0.234 AC XY: 17387 AN XY: 74252

African (AFR) AF: 0.423 AC: 17517 AN: 41388

American (AMR) AF: 0.209 AC: 3186 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 744 AN: 3470

East Asian (EAS) AF: 0.187 AC: 966 AN: 5172

South Asian (SAS) AF: 0.152 AC: 732 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1303 AN: 10526

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11289 AN: 67970

Other (OTH) AF: 0.244 AC: 515 AN: 2110

Alfa AF: 0.188 Hom.: 10753

Bravo AF: 0.253

Asia WGS AF: 0.202 AC: 701 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs10943944; hg19: chr6-84211936;