rs1535257

Variant names:

• chr6-88184703-A-C
• rs1535257
• ENST00000648572.1:n.991-6269T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-88184703-A-C
• chr6-88184703-A-G

Variant summary

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

The ENST00000648572.1(ENSG00000234426):​n.991-6269T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,974 control chromosomes in the GnomAD database, including 9,134 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 0.31 (9134 hom., cov: 32)
• Consequence: ENSG00000234426 ENST00000648572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 4 publications found

Genes affected

ENSG00000234426 (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 = 0.551 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
ENSG00000234426	ENST00000648572.1	n.991-6269T>G		intron_variant	Intron 6 of 6
ENSG00000298549	ENST00000756364.1	n.129-26894A>C		intron_variant	Intron 1 of 2
ENSG00000298549	ENST00000756365.1	n.571+14434A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46499 AN: 151856 Hom.: 9099 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.307 AC: 46592 AN: 151974 Hom.: 9134 Cov.: 32 AF XY: 0.307 AC XY: 22807 AN XY: 74290

African (AFR) AF: 0.557 AC: 23085 AN: 41414

American (AMR) AF: 0.255 AC: 3896 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3466

East Asian (EAS) AF: 0.185 AC: 956 AN: 5172

South Asian (SAS) AF: 0.248 AC: 1196 AN: 4818

European-Finnish (FIN) AF: 0.278 AC: 2931 AN: 10560

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13167 AN: 67956

Other (OTH) AF: 0.272 AC: 574 AN: 2108

Alfa AF: 0.221 Hom.: 18942

Bravo AF: 0.315

Asia WGS AF: 0.294 AC: 1026 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	7.8
DANN	Benign	0.66
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1535257; hg19: chr6-88894422; COSMIC: COSV69412265;