rs35678510

Variant names:

• chr6-17066915-G-A
• rs35678510
• ENST00000798149.1:n.225+27231C>T

Variant summary

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

The ENST00000798149.1(ENSG00000287359):​n.225+27231C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0514 in 152,198 control chromosomes in the GnomAD database, including 279 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 0.051 (279 hom., cov: 33)
• Consequence: ENSG00000287359 ENST00000798149.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 0 publications found

Genes affected

ENSG00000287359 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901269	XR_007059481.1	n.39-6081C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287359	ENST00000798149.1	n.225+27231C>T		intron_variant	Intron 1 of 1
ENSG00000287359	ENST00000798150.1	n.224+7251C>T		intron_variant	Intron 2 of 2
ENSG00000287359	ENST00000798151.1	n.212-6081C>T		intron_variant	Intron 1 of 1
ENSG00000287359	ENST00000798152.1	n.487-6081C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0514 AC: 7822 AN: 152080 Hom.: 279 Cov.: 33

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.0436

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.0794

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0514 AC: 7822 AN: 152198 Hom.: 279 Cov.: 33 AF XY: 0.0500 AC XY: 3719 AN XY: 74412

African (AFR) AF: 0.0140 AC: 581 AN: 41556

American (AMR) AF: 0.0480 AC: 733 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0436 AC: 151 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00850 AC: 41 AN: 4824

European-Finnish (FIN) AF: 0.0794 AC: 840 AN: 10582

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0772 AC: 5250 AN: 68004

Other (OTH) AF: 0.0464 AC: 98 AN: 2112

Alfa AF: 0.0614 Hom.: 135

Bravo AF: 0.0469

Asia WGS AF: 0.00491 AC: 17 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.85
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs35678510; hg19: chr6-17067146; COSMIC: COSV62123081;