rs7528859

Variant names:

• chr1-5600949-T-A
• rs7528859
• ENST00000413887.1:n.156-13374A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637702.1(ENSG00000236948):​n.116-37594A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,948 control chromosomes in the GnomAD database, including 16,688 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 0.45 (16688 hom., cov: 33)
• Consequence: ENSG00000236948 ENST00000637702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895

Genes affected

ENSG00000236948 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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
ENSG00000236948	ENST00000413887.1	n.156-13374A>T		intron_variant	Intron 1 of 1	5
ENSG00000236948	ENST00000637702.1	n.116-37594A>T		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67915 AN: 151830 Hom.: 16656 Cov.: 33

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.447 AC: 67995 AN: 151948 Hom.: 16688 Cov.: 33 AF XY: 0.440 AC XY: 32663 AN XY: 74248

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.436

Alfa AF: 0.417 Hom.: 1781

Bravo AF: 0.465

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.39
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7528859; hg19: chr1-5661009;