rs1908423

Variant names:

• chr4-74512220-C-G
• rs1908423

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0728 in 152,068 control chromosomes in the GnomAD database, including 472 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 0.073 (472 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 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: 0.0727 AC: 11043 AN: 151952 Hom.: 466 Cov.: 32

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0529

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0728 AC: 11064 AN: 152068 Hom.: 472 Cov.: 32 AF XY: 0.0761 AC XY: 5656 AN XY: 74338

Gnomad4 AFR AF: 0.0884

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0581

Gnomad4 NFE AF: 0.0529

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0610 Hom.: 41

Bravo AF: 0.0735

Asia WGS AF: 0.146 AC: 508 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1908423; hg19: chr4-75377937;