3-106032178-G-C

Variant names:

• chr3-106032178-G-C
• rs6437640
• ENST00000833900.1:n.74-10987C>G

Variant summary

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

The ENST00000833900.1(ENSG00000308417):​n.74-10987C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,932 control chromosomes in the GnomAD database, including 12,712 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 0.33 (12712 hom., cov: 31)
• Consequence: ENSG00000308417 ENST00000833900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 1 publications found

Genes affected

ENSG00000308417 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 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
ENSG00000308417	ENST00000833900.1	n.74-10987C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50429 AN: 151816 Hom.: 12671 Cov.: 31

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0721

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.333 AC: 50540 AN: 151932 Hom.: 12712 Cov.: 31 AF XY: 0.329 AC XY: 24450 AN XY: 74266

African (AFR) AF: 0.706 AC: 29248 AN: 41400

American (AMR) AF: 0.312 AC: 4760 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3470

East Asian (EAS) AF: 0.0721 AC: 373 AN: 5174

South Asian (SAS) AF: 0.162 AC: 777 AN: 4804

European-Finnish (FIN) AF: 0.204 AC: 2162 AN: 10574

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11723 AN: 67932

Other (OTH) AF: 0.303 AC: 639 AN: 2110

Alfa AF: 0.270 Hom.: 1013

Bravo AF: 0.360

Asia WGS AF: 0.157 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.038
DANN	Benign	0.46
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs6437640; hg19: chr3-105751025;