7-4313256-G-C

Variant names:

• chr7-4313256-G-C
• rs2005745

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 0.15 (2018 hom., cov: 18)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.153 AC: 21154 AN: 138518 Hom.: 2009 Cov.: 18

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.0900

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.153 AC: 21178 AN: 138622 Hom.: 2018 Cov.: 18 AF XY: 0.158 AC XY: 10565 AN XY: 66676

African (AFR) AF: 0.0542 AC: 1928 AN: 35560

American (AMR) AF: 0.269 AC: 3627 AN: 13490

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 417 AN: 3320

East Asian (EAS) AF: 0.159 AC: 777 AN: 4890

South Asian (SAS) AF: 0.177 AC: 665 AN: 3752

European-Finnish (FIN) AF: 0.223 AC: 2056 AN: 9222

Middle Eastern (MID) AF: 0.0971 AC: 27 AN: 278

European-Non Finnish (NFE) AF: 0.171 AC: 11164 AN: 65416

Other (OTH) AF: 0.146 AC: 266 AN: 1828

Alfa AF: 0.147 Hom.: 226

Bravo AF: 0.151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.0
DANN	Benign	0.27
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs2005745; hg19: chr7-4352887; COSMIC: COSV53494300;