rs2223793

Variant names:

• chr6-84324964-C-T
• rs2223793

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 0.195 in 152,060 control chromosomes in the GnomAD database, including 5,247 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 0.19 (5247 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 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: 0.194 AC: 29548 AN: 151942 Hom.: 5211 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0684

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0761

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.195 AC: 29641 AN: 152060 Hom.: 5247 Cov.: 32 AF XY: 0.193 AC XY: 14326 AN XY: 74326

African (AFR) AF: 0.478 AC: 19799 AN: 41406

American (AMR) AF: 0.126 AC: 1927 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0962 AC: 334 AN: 3472

East Asian (EAS) AF: 0.120 AC: 619 AN: 5166

South Asian (SAS) AF: 0.126 AC: 609 AN: 4818

European-Finnish (FIN) AF: 0.0684 AC: 724 AN: 10592

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0761 AC: 5172 AN: 68006

Other (OTH) AF: 0.172 AC: 363 AN: 2110

Alfa AF: 0.112 Hom.: 3379

Bravo AF: 0.211

Asia WGS AF: 0.156 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.99
DANN	Benign	0.41
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs2223793; hg19: chr6-85034682;