rs4520040

Variant names:

• chr6-103984290-G-A
• rs4520040
• ENST00000843032.1:n.148+1633C>T

Variant summary

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

The ENST00000843032.1(ENSG00000309686):​n.148+1633C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0869 in 151,976 control chromosomes in the GnomAD database, including 938 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 0.087 (938 hom., cov: 31)
• Consequence: ENSG00000309686 ENST00000843032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 8 publications found

Genes affected

ENSG00000309686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 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
ENSG00000309686	ENST00000843032.1	n.148+1633C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13144 AN: 151858 Hom.: 926 Cov.: 31

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0438

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0869 AC: 13201 AN: 151976 Hom.: 938 Cov.: 31 AF XY: 0.0926 AC XY: 6878 AN XY: 74272

African (AFR) AF: 0.0976 AC: 4051 AN: 41504

American (AMR) AF: 0.157 AC: 2386 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3468

East Asian (EAS) AF: 0.371 AC: 1904 AN: 5132

South Asian (SAS) AF: 0.0765 AC: 369 AN: 4822

European-Finnish (FIN) AF: 0.118 AC: 1252 AN: 10594

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0438 AC: 2977 AN: 67932

Other (OTH) AF: 0.0841 AC: 177 AN: 2104

Alfa AF: 0.0628 Hom.: 1973

Bravo AF: 0.0923

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.55
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4520040; hg19: chr6-104432165;