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. The variant received -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
• Publications: 35 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.431 AC: 9175 AN: 21294

American (AMR) AF: 0.786 AC: 9022 AN: 11478

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2779 AN: 3270

East Asian (EAS) AF: 0.935 AC: 4061 AN: 4344

South Asian (SAS) AF: 0.795 AC: 2940 AN: 3696

European-Finnish (FIN) AF: 0.808 AC: 4523 AN: 5598

Middle Eastern (MID) AF: 0.874 AC: 194 AN: 222

European-Non Finnish (NFE) AF: 0.803 AC: 49818 AN: 62036

Other (OTH) AF: 0.753 AC: 1198 AN: 1590

Alfa AF: 0.359 Hom.: 3975

Bravo AF: 0.620

Asia WGS AF: 0.808 AC: 2797 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.67
PhyloP100		-0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4970836; hg19: chr1-109821797;