rs6478338

Variant names:

• chr9-117945495-T-C
• rs6478338
• ENST00000665764.1:n.*17-26604T>C

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*17-26604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,058 control chromosomes in the GnomAD database, including 3,346 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 0.20 (3346 hom., cov: 32)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 1 publications found

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.28 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
ENSG00000285082	ENST00000665764.1	n.*17-26604T>C		intron_variant	Intron 2 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*16+97340T>C		intron_variant	Intron 2 of 5			ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1053+97340T>C		intron_variant	Intron 7 of 12

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30608 AN: 151940 Hom.: 3345 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.201 AC: 30622 AN: 152058 Hom.: 3346 Cov.: 32 AF XY: 0.198 AC XY: 14698 AN XY: 74324

African (AFR) AF: 0.284 AC: 11760 AN: 41438

American (AMR) AF: 0.137 AC: 2092 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1044 AN: 5160

South Asian (SAS) AF: 0.173 AC: 834 AN: 4822

European-Finnish (FIN) AF: 0.134 AC: 1422 AN: 10598

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.180 AC: 12213 AN: 67986

Other (OTH) AF: 0.200 AC: 422 AN: 2108

Alfa AF: 0.194 Hom.: 627

Bravo AF: 0.205

Asia WGS AF: 0.219 AC: 764 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	4.3
DANN	Benign	0.67
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6478338; hg19: chr9-120707773;