rs7673587

Variant names:

• chr4-154559282-C-T
• rs7673587

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 0.246 in 151,930 control chromosomes in the GnomAD database, including 5,376 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 0.25 (5376 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 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: 0.246 AC: 37386 AN: 151812 Hom.: 5378 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.246 AC: 37364 AN: 151930 Hom.: 5376 Cov.: 31 AF XY: 0.243 AC XY: 18016 AN XY: 74236

African (AFR) AF: 0.108 AC: 4491 AN: 41432

American (AMR) AF: 0.221 AC: 3382 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1139 AN: 3466

East Asian (EAS) AF: 0.140 AC: 721 AN: 5148

South Asian (SAS) AF: 0.335 AC: 1614 AN: 4812

European-Finnish (FIN) AF: 0.243 AC: 2563 AN: 10548

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.333 AC: 22615 AN: 67938

Other (OTH) AF: 0.279 AC: 590 AN: 2112

Alfa AF: 0.268 Hom.: 764

Bravo AF: 0.236

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs7673587; hg19: chr4-155480434;