rs35951010

Variant names:

• chr6-88135012-G-C
• rs35951010
• ENST00000756364.1:n.128+9415G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-88135012-G-C
• chr6-88135012-G-T

Variant summary

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

The ENST00000756364.1(ENSG00000298549):​n.128+9415G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,178 control chromosomes in the GnomAD database, including 1,359 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 0.11 (1359 hom., cov: 32)
• Consequence: ENSG00000298549 ENST00000756364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 2 publications found

Genes affected

ENSG00000298549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 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
ENSG00000298549	ENST00000756364.1	n.128+9415G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17025 AN: 152060 Hom.: 1358 Cov.: 32

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0788

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.112 AC: 17023 AN: 152178 Hom.: 1359 Cov.: 32 AF XY: 0.114 AC XY: 8509 AN XY: 74386

African (AFR) AF: 0.0255 AC: 1061 AN: 41540

American (AMR) AF: 0.0786 AC: 1202 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3472

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5186

South Asian (SAS) AF: 0.166 AC: 799 AN: 4824

European-Finnish (FIN) AF: 0.222 AC: 2351 AN: 10570

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

European-Non Finnish (NFE) AF: 0.160 AC: 10900 AN: 67972

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.0762 Hom.: 98

Bravo AF: 0.0970

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	8.2
DANN	Benign	0.78
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs35951010; hg19: chr6-88844731; COSMIC: COSV65673254;