6-4379277-A-G

Variant names:

• chr6-4379277-A-G
• rs17138114
• ENST00000642310.1:n.962+49106T>C

Variant summary

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

The ENST00000642310.1(ENSG00000284823):​n.962+49106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,194 control chromosomes in the GnomAD database, including 951 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 0.10 (951 hom., cov: 32)
• Consequence: ENSG00000284823 ENST00000642310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472
• Publications: 5 publications found

Genes affected

ENSG00000284823 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.166 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
ENSG00000284823	ENST00000642310.1	n.962+49106T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15681 AN: 152076 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.0865

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0644

Gnomad FIN AF: 0.0865

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.103 AC: 15712 AN: 152194 Hom.: 951 Cov.: 32 AF XY: 0.104 AC XY: 7734 AN XY: 74394

African (AFR) AF: 0.0865 AC: 3592 AN: 41542

American (AMR) AF: 0.171 AC: 2614 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3468

East Asian (EAS) AF: 0.149 AC: 772 AN: 5168

South Asian (SAS) AF: 0.0641 AC: 309 AN: 4824

European-Finnish (FIN) AF: 0.0865 AC: 917 AN: 10602

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0948 AC: 6448 AN: 67990

Other (OTH) AF: 0.123 AC: 259 AN: 2112

Alfa AF: 0.102 Hom.: 3958

Bravo AF: 0.114

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.63
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs17138114; hg19: chr6-4379511;