6-104312248-A-G

Variant names:

• chr6-104312248-A-G
• rs13213851

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 0.44 in 151,990 control chromosomes in the GnomAD database, including 15,335 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 0.44 (15335 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 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: 0.440 AC: 66796 AN: 151872 Hom.: 15334 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.440 AC: 66814 AN: 151990 Hom.: 15335 Cov.: 32 AF XY: 0.437 AC XY: 32446 AN XY: 74274

African (AFR) AF: 0.298 AC: 12342 AN: 41450

American (AMR) AF: 0.452 AC: 6892 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3470

East Asian (EAS) AF: 0.529 AC: 2737 AN: 5174

South Asian (SAS) AF: 0.437 AC: 2106 AN: 4818

European-Finnish (FIN) AF: 0.467 AC: 4926 AN: 10558

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.508 AC: 34494 AN: 67966

Other (OTH) AF: 0.499 AC: 1054 AN: 2114

Alfa AF: 0.460 Hom.: 9521

Bravo AF: 0.437

Asia WGS AF: 0.450 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.073
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs13213851; hg19: chr6-104760123;