6-103389640-T-C

Variant names:

• chr6-103389640-T-C
• rs724845

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 0.214 in 152,094 control chromosomes in the GnomAD database, including 3,583 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 0.21 (3583 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32477 AN: 151976 Hom.: 3572 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.214 AC: 32517 AN: 152094 Hom.: 3583 Cov.: 32 AF XY: 0.211 AC XY: 15686 AN XY: 74348

African (AFR) AF: 0.199 AC: 8263 AN: 41508

American (AMR) AF: 0.231 AC: 3532 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3470

East Asian (EAS) AF: 0.106 AC: 549 AN: 5158

South Asian (SAS) AF: 0.173 AC: 836 AN: 4826

European-Finnish (FIN) AF: 0.174 AC: 1840 AN: 10600

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16004 AN: 67956

Other (OTH) AF: 0.224 AC: 474 AN: 2112

Alfa AF: 0.229 Hom.: 796

Bravo AF: 0.220

Asia WGS AF: 0.152 AC: 529 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.83
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs724845; hg19: chr6-103837515; COSMIC: COSV69417578;