rs6921460

Variant names:

• chr6-144077022-T-C
• rs6921460

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 0.242 in 151,992 control chromosomes in the GnomAD database, including 4,527 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 0.24 (4527 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.328 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: 0.242 AC: 36732 AN: 151874 Hom.: 4522 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.242 AC: 36756 AN: 151992 Hom.: 4527 Cov.: 31 AF XY: 0.248 AC XY: 18397 AN XY: 74322

African (AFR) AF: 0.244 AC: 10122 AN: 41446

American (AMR) AF: 0.336 AC: 5123 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1036 AN: 3468

East Asian (EAS) AF: 0.295 AC: 1523 AN: 5162

South Asian (SAS) AF: 0.284 AC: 1369 AN: 4814

European-Finnish (FIN) AF: 0.231 AC: 2444 AN: 10560

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14268 AN: 67972

Other (OTH) AF: 0.274 AC: 578 AN: 2110

Alfa AF: 0.222 Hom.: 1791

Bravo AF: 0.252

Asia WGS AF: 0.267 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.46
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs6921460; hg19: chr6-144398159; COSMIC: COSV60289825;