rs979233

Variant names:

• chr5-42375141-A-C
• rs979233

Your query was ambiguous. Multiple possible variants found:

• chr5-42375141-A-C
• chr5-42375141-A-G
• chr5-42375141-A-T

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 0.509 in 151,994 control chromosomes in the GnomAD database, including 20,901 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 0.51 (20901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 12 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 (EAS) allele frequency at 95% confidence interval = 0.866 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: 0.509 AC: 77313 AN: 151876 Hom.: 20887 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.509 AC: 77372 AN: 151994 Hom.: 20901 Cov.: 32 AF XY: 0.515 AC XY: 38252 AN XY: 74282

African (AFR) AF: 0.346 AC: 14356 AN: 41466

American (AMR) AF: 0.529 AC: 8076 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1847 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4569 AN: 5150

South Asian (SAS) AF: 0.657 AC: 3169 AN: 4824

European-Finnish (FIN) AF: 0.584 AC: 6159 AN: 10552

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37658 AN: 67950

Other (OTH) AF: 0.499 AC: 1055 AN: 2114

Alfa AF: 0.550 Hom.: 78347

Bravo AF: 0.497

Asia WGS AF: 0.748 AC: 2601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.35
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs979233; hg19: chr5-42375243;