4-154969089-C-T

Variant names:

• chr4-154969089-C-T
• rs6837016

Variant summary

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

The variant allele was found at a frequency of 0.606 in 151,982 control chromosomes in the GnomAD database, including 28,285 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 0.61 (28285 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 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

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91934 AN: 151864 Hom.: 28242 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.606 AC: 92026 AN: 151982 Hom.: 28285 Cov.: 31 AF XY: 0.608 AC XY: 45175 AN XY: 74288

African (AFR) AF: 0.697 AC: 28899 AN: 41458

American (AMR) AF: 0.572 AC: 8733 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1722 AN: 3460

East Asian (EAS) AF: 0.743 AC: 3832 AN: 5160

South Asian (SAS) AF: 0.720 AC: 3469 AN: 4816

European-Finnish (FIN) AF: 0.606 AC: 6395 AN: 10558

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37002 AN: 67942

Other (OTH) AF: 0.576 AC: 1215 AN: 2110

Alfa AF: 0.565 Hom.: 9918

Bravo AF: 0.603

Asia WGS AF: 0.690 AC: 2391 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.33
DANN	Benign	0.54
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6837016; hg19: chr4-155890241;