chr5-105644654-T-C

Variant names:

• chr5-105644654-T-C
• rs6872786

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 0.643 in 151,924 control chromosomes in the GnomAD database, including 31,971 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 0.64 (31971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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: 0.643 AC: 97551 AN: 151806 Hom.: 31920 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.643 AC: 97665 AN: 151924 Hom.: 31971 Cov.: 32 AF XY: 0.637 AC XY: 47284 AN XY: 74252

African (AFR) AF: 0.713 AC: 29566 AN: 41456

American (AMR) AF: 0.697 AC: 10631 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2195 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1641 AN: 5154

South Asian (SAS) AF: 0.669 AC: 3225 AN: 4820

European-Finnish (FIN) AF: 0.513 AC: 5411 AN: 10540

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.632 AC: 42904 AN: 67916

Other (OTH) AF: 0.656 AC: 1384 AN: 2110

Alfa AF: 0.639 Hom.: 131123

Bravo AF: 0.655

Asia WGS AF: 0.532 AC: 1851 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.84
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6872786; hg19: chr5-104980355;