6-154010049-T-C

Variant names:

• chr6-154010049-T-C
• rs1319339

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 0.113 in 152,080 control chromosomes in the GnomAD database, including 1,275 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 0.11 (1275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.80
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17170 AN: 151962 Hom.: 1275 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.0807

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0572

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.0909

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

GnomAD4 genome AF: 0.113 AC: 17167 AN: 152080 Hom.: 1275 Cov.: 32 AF XY: 0.109 AC XY: 8071 AN XY: 74324

African (AFR) AF: 0.0274 AC: 1138 AN: 41536

American (AMR) AF: 0.0805 AC: 1229 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0574 AC: 277 AN: 4824

European-Finnish (FIN) AF: 0.180 AC: 1902 AN: 10574

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11765 AN: 67922

Other (OTH) AF: 0.0899 AC: 189 AN: 2102

Alfa AF: 0.141 Hom.: 1244

Bravo AF: 0.102

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.013
DANN	Benign	0.34
PhyloP100		-6.8
PromoterAI		-0.0044	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1319339; hg19: chr6-154331184;