chr8-56259673-T-G

Variant names:

• chr8-56259673-T-G
• rs7829319

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 0.157 in 151,746 control chromosomes in the GnomAD database, including 1,943 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 0.16 (1943 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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: 0.157 AC: 23873 AN: 151630 Hom.: 1939 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0599

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.157 AC: 23893 AN: 151746 Hom.: 1943 Cov.: 31 AF XY: 0.155 AC XY: 11517 AN XY: 74166

African (AFR) AF: 0.209 AC: 8648 AN: 41304

American (AMR) AF: 0.161 AC: 2452 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 668 AN: 3464

East Asian (EAS) AF: 0.0597 AC: 309 AN: 5180

South Asian (SAS) AF: 0.138 AC: 664 AN: 4818

European-Finnish (FIN) AF: 0.129 AC: 1353 AN: 10470

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

European-Non Finnish (NFE) AF: 0.137 AC: 9278 AN: 67948

Other (OTH) AF: 0.174 AC: 366 AN: 2108

Alfa AF: 0.156 Hom.: 527

Bravo AF: 0.164

Asia WGS AF: 0.133 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.21
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7829319; hg19: chr8-57172232;