4-122699757-T-G

Variant names:

• chr4-122699757-T-G
• rs309414

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 0.658 in 152,122 control chromosomes in the GnomAD database, including 34,024 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 0.66 (34024 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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: 0.658 AC: 99999 AN: 152004 Hom.: 33996 Cov.: 33

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.658 AC: 100080 AN: 152122 Hom.: 34024 Cov.: 33 AF XY: 0.655 AC XY: 48724 AN XY: 74360

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.660

Alfa AF: 0.615 Hom.: 47686

Bravo AF: 0.685

Asia WGS AF: 0.880 AC: 3058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs309414; hg19: chr4-123620912;