rs6840361

Variant names:

• chr4-162816969-C-G
• rs6840361
• ENST00000661387.1:n.165+75190C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661387.1(ENSG00000248431):​n.165+75190C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 151,804 control chromosomes in the GnomAD database, including 1,196 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 0.11 (1196 hom., cov: 32)
• Consequence: ENSG00000248431 ENST00000661387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

Genes affected

ENSG00000248431 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 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
ENSG00000248431	ENST00000661387.1	n.165+75190C>G		intron_variant	Intron 2 of 3
ENSG00000287072	ENST00000662873.1	n.157+3901G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16649 AN: 151688 Hom.: 1188 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.110 AC: 16681 AN: 151804 Hom.: 1196 Cov.: 32 AF XY: 0.107 AC XY: 7938 AN XY: 74184

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0802

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0847

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0271

Gnomad4 NFE AF: 0.0724

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0898 Hom.: 113

Bravo AF: 0.117

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6840361; hg19: chr4-163738121;