rs335378

Variant names:

• chr6-155359727-A-G
• rs335378
• ENST00000809830.1:n.58-18297A>G

Variant summary

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

The ENST00000809830.1(ENSG00000305252):​n.58-18297A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,000 control chromosomes in the GnomAD database, including 3,100 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 0.16 (3100 hom., cov: 32)
• Consequence: ENSG00000305252 ENST00000809830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 2 publications found

Genes affected

ENSG00000305252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 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
ENSG00000305252	ENST00000809830.1	n.58-18297A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24881 AN: 151882 Hom.: 3080 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.0938

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.164 AC: 24958 AN: 152000 Hom.: 3100 Cov.: 32 AF XY: 0.164 AC XY: 12185 AN XY: 74302

African (AFR) AF: 0.351 AC: 14536 AN: 41466

American (AMR) AF: 0.0912 AC: 1393 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0938 AC: 325 AN: 3464

East Asian (EAS) AF: 0.255 AC: 1321 AN: 5180

South Asian (SAS) AF: 0.101 AC: 485 AN: 4824

European-Finnish (FIN) AF: 0.114 AC: 1208 AN: 10586

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0784 AC: 5323 AN: 67890

Other (OTH) AF: 0.124 AC: 261 AN: 2108

Alfa AF: 0.116 Hom.: 3470

Bravo AF: 0.171

Asia WGS AF: 0.222 AC: 770 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs335378; hg19: chr6-155680861;