rs1883637

Variant names:

• chr6-35526822-C-T
• rs1883637
• ENST00000722033.1:n.122-18046C>T

Variant summary

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

The ENST00000722033.1(ENSG00000228559):​n.122-18046C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0655 in 152,208 control chromosomes in the GnomAD database, including 477 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 0.066 (477 hom., cov: 31)
• Consequence: ENSG00000228559 ENST00000722033.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 0 publications found

Genes affected

ENSG00000228559 (HGNC:58100):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.115 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
ENSG00000228559	ENST00000722033.1	n.122-18046C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9981 AN: 152090 Hom.: 476 Cov.: 31

Gnomad AFR AF: 0.0178

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.0618

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

GnomAD4 genome AF: 0.0655 AC: 9977 AN: 152208 Hom.: 477 Cov.: 31 AF XY: 0.0632 AC XY: 4702 AN XY: 74420

African (AFR) AF: 0.0178 AC: 738 AN: 41544

American (AMR) AF: 0.119 AC: 1825 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3470

East Asian (EAS) AF: 0.0613 AC: 317 AN: 5168

South Asian (SAS) AF: 0.0655 AC: 316 AN: 4824

European-Finnish (FIN) AF: 0.0413 AC: 438 AN: 10602

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0899 AC: 6114 AN: 68016

Other (OTH) AF: 0.0612 AC: 129 AN: 2108

Alfa AF: 0.0756 Hom.: 83

Bravo AF: 0.0702

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.55
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1883637; hg19: chr6-35494599;