6-108721256-T-C

Variant names:

• chr6-108721256-T-C
• rs484754

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 0.765 in 152,136 control chromosomes in the GnomAD database, including 45,473 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 0.76 (45473 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 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: 0.764 AC: 116178 AN: 152018 Hom.: 45405 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.764 AC: 116308 AN: 152136 Hom.: 45473 Cov.: 31 AF XY: 0.767 AC XY: 57056 AN XY: 74364

African (AFR) AF: 0.936 AC: 38890 AN: 41538

American (AMR) AF: 0.752 AC: 11485 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3470

East Asian (EAS) AF: 0.736 AC: 3803 AN: 5166

South Asian (SAS) AF: 0.838 AC: 4041 AN: 4820

European-Finnish (FIN) AF: 0.694 AC: 7330 AN: 10562

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46099 AN: 67986

Other (OTH) AF: 0.769 AC: 1627 AN: 2116

Alfa AF: 0.713 Hom.: 58204

Bravo AF: 0.773

Asia WGS AF: 0.827 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs484754; hg19: chr6-109042459;