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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0904 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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.0699

Gnomad4 ASJ AF: 0.0859

Gnomad4 EAS AF: 0.000969

Gnomad4 SAS AF: 0.0464

Gnomad4 FIN AF: 0.0266

Gnomad4 NFE AF: 0.0394

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0229 Hom.: 26

Bravo AF: 0.0990

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2264670; hg19: chr7-112736754;