6-37550405-C-T

Variant names:

• chr6-37550405-C-T
• rs914351
• ENST00000414875.2:n.706-163C>T

Variant summary

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

The ENST00000414875.2(ENSG00000227920):​n.706-163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,252 control chromosomes in the GnomAD database, including 4,403 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 0.23 (4403 hom., cov: 34)
• Consequence: ENSG00000227920 ENST00000414875.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778

Genes affected

ENSG00000227920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 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
ENSG00000227920	ENST00000414875.2	n.706-163C>T		intron_variant	Intron 4 of 4	5
ENSG00000227920	ENST00000656831.1	n.*104C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34483 AN: 152134 Hom.: 4391 Cov.: 34

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.227 AC: 34500 AN: 152252 Hom.: 4403 Cov.: 34 AF XY: 0.227 AC XY: 16900 AN XY: 74450

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.241

Alfa AF: 0.217 Hom.: 7827

Bravo AF: 0.226

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	0.15
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs914351; hg19: chr6-37518181;