rs7823896

Variant names:

• chr8-109205037-T-C
• rs7823896

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 0.275 in 152,130 control chromosomes in the GnomAD database, including 9,409 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 0.27 (9409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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: 0.274 AC: 41680 AN: 152012 Hom.: 9369 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0679

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.275 AC: 41770 AN: 152130 Hom.: 9409 Cov.: 32 AF XY: 0.268 AC XY: 19909 AN XY: 74366

African (AFR) AF: 0.620 AC: 25687 AN: 41450

American (AMR) AF: 0.205 AC: 3131 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3472

East Asian (EAS) AF: 0.0550 AC: 285 AN: 5178

South Asian (SAS) AF: 0.171 AC: 823 AN: 4824

European-Finnish (FIN) AF: 0.0679 AC: 720 AN: 10606

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9821 AN: 68000

Other (OTH) AF: 0.280 AC: 590 AN: 2110

Alfa AF: 0.195 Hom.: 13132

Bravo AF: 0.299

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.64
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7823896; hg19: chr8-110217266; COSMIC: COSV56999503;