chr7-97784798-C-T

Variant names:

• chr7-97784798-C-T
• rs460

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 0.261 in 151,946 control chromosomes in the GnomAD database, including 5,856 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 0.26 (5856 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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: 0.261 AC: 39558 AN: 151828 Hom.: 5852 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.261 AC: 39608 AN: 151946 Hom.: 5856 Cov.: 32 AF XY: 0.255 AC XY: 18959 AN XY: 74286

African (AFR) AF: 0.411 AC: 17026 AN: 41396

American (AMR) AF: 0.199 AC: 3033 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3470

East Asian (EAS) AF: 0.109 AC: 564 AN: 5160

South Asian (SAS) AF: 0.265 AC: 1275 AN: 4810

European-Finnish (FIN) AF: 0.144 AC: 1524 AN: 10558

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14341 AN: 67966

Other (OTH) AF: 0.264 AC: 559 AN: 2114

Alfa AF: 0.229 Hom.: 13513

Bravo AF: 0.270

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.0
DANN	Benign	0.43
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs460; hg19: chr7-97414110;