6-99003195-T-C

Variant names:

• chr6-99003195-T-C
• rs2572096

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.102 in 152,144 control chromosomes in the GnomAD database, including 1,057 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 0.10 (1057 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 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: 0.102 AC: 15544 AN: 152026 Hom.: 1049 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.102 AC: 15573 AN: 152144 Hom.: 1057 Cov.: 31 AF XY: 0.104 AC XY: 7707 AN XY: 74404

African (AFR) AF: 0.175 AC: 7266 AN: 41480

American (AMR) AF: 0.0689 AC: 1053 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1396 AN: 5156

South Asian (SAS) AF: 0.111 AC: 536 AN: 4816

European-Finnish (FIN) AF: 0.0581 AC: 616 AN: 10610

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0606 AC: 4119 AN: 68012

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.0797 Hom.: 243

Bravo AF: 0.108

Asia WGS AF: 0.215 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	12
DANN	Benign	0.68
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2572096; hg19: chr6-99451071; COSMIC: COSV69415390;