rs1908423

Positions:

• chr4-74512220-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;