rs400837

Variant names:

• chr6-166997520-T-C
• rs400837
• ENST00000444102.1:n.148+1398A>G

Variant summary

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

The ENST00000444102.1(ENSG00000227598):​n.148+1398A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,160 control chromosomes in the GnomAD database, including 14,739 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 0.42 (14739 hom., cov: 33)
• Consequence: ENSG00000227598 ENST00000444102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 21 publications found

Genes affected

ENSG00000227598 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 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
ENSG00000227598	ENST00000444102.1	n.148+1398A>G		intron_variant	Intron 1 of 2	5
ENSG00000285730	ENST00000649589.1	n.156-939A>G		intron_variant	Intron 1 of 1
ENSG00000227598	ENST00000832409.1	n.166+1398A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64638 AN: 152042 Hom.: 14738 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.425 AC: 64650 AN: 152160 Hom.: 14739 Cov.: 33 AF XY: 0.420 AC XY: 31210 AN XY: 74384

African (AFR) AF: 0.268 AC: 11130 AN: 41544

American (AMR) AF: 0.388 AC: 5930 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1636 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1964 AN: 5182

South Asian (SAS) AF: 0.305 AC: 1471 AN: 4828

European-Finnish (FIN) AF: 0.467 AC: 4933 AN: 10562

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36186 AN: 67976

Other (OTH) AF: 0.410 AC: 866 AN: 2110

Alfa AF: 0.499 Hom.: 9937

Bravo AF: 0.410

Asia WGS AF: 0.336 AC: 1171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.7
DANN	Benign	0.61
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs400837; hg19: chr6-167411008;