rs2264670

Variant names:

• chr7-113096699-T-A
• rs2264670

Your query was ambiguous. Multiple possible variants found:

• chr7-113096699-T-A
• chr7-113096699-T-C

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 0.0904 in 152,018 control chromosomes in the GnomAD database, including 1,099 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 0.090 (1099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 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: 0.0904 AC: 13727 AN: 151900 Hom.: 1098 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.000967

Gnomad SAS AF: 0.0466

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0394

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0904 AC: 13742 AN: 152018 Hom.: 1099 Cov.: 32 AF XY: 0.0887 AC XY: 6592 AN XY: 74326

African (AFR) AF: 0.213 AC: 8840 AN: 41438

American (AMR) AF: 0.0699 AC: 1065 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 298 AN: 3470

East Asian (EAS) AF: 0.000969 AC: 5 AN: 5160

South Asian (SAS) AF: 0.0464 AC: 224 AN: 4824

European-Finnish (FIN) AF: 0.0266 AC: 282 AN: 10604

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0394 AC: 2681 AN: 67960

Other (OTH) AF: 0.105 AC: 222 AN: 2112

Alfa AF: 0.0229 Hom.: 26

Bravo AF: 0.0990

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.84
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2264670; hg19: chr7-112736754;