rs1229979

Variant names:

• chr4-99334796-C-T
• rs1229979

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 0.233 in 152,094 control chromosomes in the GnomAD database, including 4,908 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 (4908 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 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: 0.233 AC: 35419 AN: 151976 Hom.: 4905 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.233 AC: 35430 AN: 152094 Hom.: 4908 Cov.: 32 AF XY: 0.231 AC XY: 17192 AN XY: 74350

African (AFR) AF: 0.117 AC: 4839 AN: 41506

American (AMR) AF: 0.198 AC: 3032 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3470

East Asian (EAS) AF: 0.0213 AC: 110 AN: 5170

South Asian (SAS) AF: 0.196 AC: 942 AN: 4818

European-Finnish (FIN) AF: 0.372 AC: 3931 AN: 10564

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21130 AN: 67964

Other (OTH) AF: 0.207 AC: 436 AN: 2108

Alfa AF: 0.276 Hom.: 6963

Bravo AF: 0.213

Asia WGS AF: 0.113 AC: 393 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.70
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1229979; hg19: chr4-100255953;