chr5-23742867-G-A

Variant names:

• chr5-23742867-G-A
• rs3932338

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 0.487 in 151,970 control chromosomes in the GnomAD database, including 19,729 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 0.49 (19729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 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: 0.487 AC: 73927 AN: 151852 Hom.: 19732 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.487 AC: 73944 AN: 151970 Hom.: 19729 Cov.: 32 AF XY: 0.488 AC XY: 36231 AN XY: 74238

African (AFR) AF: 0.257 AC: 10643 AN: 41478

American (AMR) AF: 0.565 AC: 8624 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2204 AN: 3466

East Asian (EAS) AF: 0.377 AC: 1939 AN: 5142

South Asian (SAS) AF: 0.522 AC: 2516 AN: 4824

European-Finnish (FIN) AF: 0.606 AC: 6387 AN: 10546

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39735 AN: 67944

Other (OTH) AF: 0.523 AC: 1101 AN: 2104

Alfa AF: 0.559 Hom.: 93842

Bravo AF: 0.478

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs3932338; hg19: chr5-23742976;