rs10807387

Variant names:

• chr6-48128646-T-C
• rs10807387

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 0.192 in 152,064 control chromosomes in the GnomAD database, including 3,253 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 0.19 (3253 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 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: 0.191 AC: 29087 AN: 151946 Hom.: 3247 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.192 AC: 29121 AN: 152064 Hom.: 3253 Cov.: 32 AF XY: 0.193 AC XY: 14322 AN XY: 74322

African (AFR) AF: 0.309 AC: 12808 AN: 41456

American (AMR) AF: 0.220 AC: 3357 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3470

East Asian (EAS) AF: 0.164 AC: 846 AN: 5170

South Asian (SAS) AF: 0.154 AC: 743 AN: 4810

European-Finnish (FIN) AF: 0.124 AC: 1312 AN: 10598

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8801 AN: 67994

Other (OTH) AF: 0.190 AC: 401 AN: 2114

Alfa AF: 0.162 Hom.: 294

Bravo AF: 0.203

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.72
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10807387; hg19: chr6-48096382;