rs6550435

Variant names:

• chr3-36822998-T-G
• rs6550435
• ENST00000631338.1:n.*153A>C

Variant summary

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

The ENST00000631338.1(ENSG00000281100):​n.*153A>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,950 control chromosomes in the GnomAD database, including 10,919 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 0.37 (10919 hom., cov: 31)
• Consequence: ENSG00000281100 ENST00000631338.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.515
• Publications: 30 publications found

Genes affected

ENSG00000281100 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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
ENSG00000281100	ENST00000631338.1	n.*153A>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56209 AN: 151832 Hom.: 10904 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0632

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.370 AC: 56281 AN: 151950 Hom.: 10919 Cov.: 31 AF XY: 0.364 AC XY: 27048 AN XY: 74280

African (AFR) AF: 0.453 AC: 18770 AN: 41392

American (AMR) AF: 0.368 AC: 5619 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1050 AN: 3470

East Asian (EAS) AF: 0.0632 AC: 327 AN: 5176

South Asian (SAS) AF: 0.292 AC: 1403 AN: 4808

European-Finnish (FIN) AF: 0.299 AC: 3158 AN: 10558

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24802 AN: 67948

Other (OTH) AF: 0.351 AC: 741 AN: 2110

Alfa AF: 0.371 Hom.: 20254

Bravo AF: 0.378

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs6550435; hg19: chr3-36864489;