rs3920615

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-6134817-T-C
• chr10-6134817-T-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841432.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309490	ENST00000841432.1		n.621+6201A>G		intron	N/A
	ENSG00000309490	ENST00000841433.1		n.618+6201A>G		intron	N/A
	ENSG00000309490	ENST00000841434.1		n.752+6048A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3920615;

hg19: chr10-6176780;