4-74512220-C-G

Variant names:

• chr4-74512220-C-G
• rs1908423

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 0.0728 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0884 AC: 3667 AN: 41484

American (AMR) AF: 0.102 AC: 1559 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3468

East Asian (EAS) AF: 0.103 AC: 531 AN: 5178

South Asian (SAS) AF: 0.148 AC: 711 AN: 4810

European-Finnish (FIN) AF: 0.0581 AC: 615 AN: 10586

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0529 AC: 3597 AN: 67946

Other (OTH) AF: 0.0762 AC: 161 AN: 2114

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1908423; hg19: chr4-75377937;