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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798149.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287359	ENST00000798149.1		n.225+27231C>T		intron	N/A
	ENSG00000287359	ENST00000798150.1		n.224+7251C>T		intron	N/A
	ENSG00000287359	ENST00000798151.1		n.212-6081C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs35678510;

hg19: chr6-17067146;

COSMIC: COSV62123081;