rs6037908

Variant names:

• chr20-4636745-A-G
• rs6037908
• ENST00000652447.1:n.88-6524T>C

Variant summary

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

The ENST00000652447.1(ENSG00000293214):​n.88-6524T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,036 control chromosomes in the GnomAD database, including 3,623 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 0.22 (3623 hom., cov: 31)
• Consequence: ENSG00000293214 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 5 publications found

Genes affected

ENSG00000293214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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
ENSG00000293214	ENST00000652447.1	n.88-6524T>C		intron_variant	Intron 1 of 1
ENSG00000293214	ENST00000773443.1	n.132-6524T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32703 AN: 151918 Hom.: 3617 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0521

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.215 AC: 32730 AN: 152036 Hom.: 3623 Cov.: 31 AF XY: 0.211 AC XY: 15716 AN XY: 74316

African (AFR) AF: 0.215 AC: 8893 AN: 41458

American (AMR) AF: 0.192 AC: 2938 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3472

East Asian (EAS) AF: 0.0523 AC: 271 AN: 5186

South Asian (SAS) AF: 0.198 AC: 952 AN: 4818

European-Finnish (FIN) AF: 0.221 AC: 2324 AN: 10538

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15732 AN: 67972

Other (OTH) AF: 0.188 AC: 397 AN: 2108

Alfa AF: 0.221 Hom.: 11363

Bravo AF: 0.208

Asia WGS AF: 0.142 AC: 492 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.63
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs6037908; hg19: chr20-4617391;