10-6134817-T-C

Variant names:

• chr10-6134817-T-C
• rs3920615
• ENST00000841432.1:n.621+6201A>G

Variant summary

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

The ENST00000841432.1(ENSG00000309490):​n.621+6201A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,140 control chromosomes in the GnomAD database, including 14,241 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 0.43 (14241 hom., cov: 33)
• Consequence: ENSG00000309490 ENST00000841432.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 5 publications found

Genes affected

ENSG00000309490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928080	XR_930619.3	n.614+6201A>G		intron_variant	Intron 1 of 2
LOC101928080	XR_930620.3	n.614+6201A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309490	ENST00000841432.1	n.621+6201A>G		intron_variant	Intron 1 of 1
ENSG00000309490	ENST00000841433.1	n.618+6201A>G		intron_variant	Intron 1 of 2
ENSG00000309490	ENST00000841434.1	n.752+6048A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65422 AN: 152022 Hom.: 14228 Cov.: 33

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.430 AC: 65479 AN: 152140 Hom.: 14241 Cov.: 33 AF XY: 0.428 AC XY: 31840 AN XY: 74392

African (AFR) AF: 0.389 AC: 16143 AN: 41486

American (AMR) AF: 0.476 AC: 7278 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2011 AN: 3468

East Asian (EAS) AF: 0.348 AC: 1802 AN: 5184

South Asian (SAS) AF: 0.400 AC: 1929 AN: 4822

European-Finnish (FIN) AF: 0.409 AC: 4326 AN: 10588

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30361 AN: 67992

Other (OTH) AF: 0.473 AC: 994 AN: 2102

Alfa AF: 0.437 Hom.: 11167

Bravo AF: 0.437

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs3920615; hg19: chr10-6176780;