chr4-10207170-C-T

Variant names:

• chr4-10207170-C-T
• rs6845818

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 0.387 in 151,990 control chromosomes in the GnomAD database, including 12,364 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 0.39 (12364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.483 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: 0.387 AC: 58794 AN: 151872 Hom.: 12363 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.387 AC: 58808 AN: 151990 Hom.: 12364 Cov.: 32 AF XY: 0.389 AC XY: 28904 AN XY: 74290

African (AFR) AF: 0.223 AC: 9256 AN: 41450

American (AMR) AF: 0.347 AC: 5309 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2105 AN: 5166

South Asian (SAS) AF: 0.500 AC: 2397 AN: 4794

European-Finnish (FIN) AF: 0.501 AC: 5283 AN: 10548

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32086 AN: 67968

Other (OTH) AF: 0.385 AC: 812 AN: 2110

Alfa AF: 0.416 Hom.: 8663

Bravo AF: 0.364

Asia WGS AF: 0.474 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.59
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6845818; hg19: chr4-10208794;