rs4312989

Variant names:

• chr6-55945684-C-T
• rs4312989

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 0.336 in 151,700 control chromosomes in the GnomAD database, including 8,867 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 0.34 (8867 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 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: 0.335 AC: 50815 AN: 151582 Hom.: 8842 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0737

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.336 AC: 50896 AN: 151700 Hom.: 8867 Cov.: 32 AF XY: 0.337 AC XY: 24992 AN XY: 74150

African (AFR) AF: 0.346 AC: 14337 AN: 41388

American (AMR) AF: 0.364 AC: 5545 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3466

East Asian (EAS) AF: 0.0731 AC: 378 AN: 5170

South Asian (SAS) AF: 0.237 AC: 1144 AN: 4820

European-Finnish (FIN) AF: 0.388 AC: 4077 AN: 10516

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23271 AN: 67812

Other (OTH) AF: 0.345 AC: 726 AN: 2104

Alfa AF: 0.331 Hom.: 4629

Bravo AF: 0.335

Asia WGS AF: 0.196 AC: 682 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs4312989; hg19: chr6-55810482;