rs4970836

Variant names:

• chr1-109279175-G-A
• rs4970836

Your query was ambiguous. Multiple possible variants found:

• chr1-109279175-G-A
• chr1-109279175-G-C

Variant summary

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

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 0.74 (30653 hom., cov: 15)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.737 AC: 84268 AN: 114284 Hom.: 30656 Cov.: 15

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.737 AC: 84266 AN: 114310 Hom.: 30653 Cov.: 15 AF XY: 0.736 AC XY: 39610 AN XY: 53796

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.753

Alfa AF: 0.650 Hom.: 3975

Bravo AF: 0.620

Asia WGS AF: 0.808 AC: 2797 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4970836; hg19: chr1-109821797;