10-72051156-G-C

Variant names:

• chr10-72051156-G-C
• rs1245577

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 0.39 in 152,098 control chromosomes in the GnomAD database, including 12,539 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 0.39 (12539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 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: 0.391 AC: 59380 AN: 151980 Hom.: 12540 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.390 AC: 59379 AN: 152098 Hom.: 12539 Cov.: 32 AF XY: 0.383 AC XY: 28476 AN XY: 74332

African (AFR) AF: 0.252 AC: 10455 AN: 41518

American (AMR) AF: 0.393 AC: 6005 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3468

East Asian (EAS) AF: 0.115 AC: 593 AN: 5164

South Asian (SAS) AF: 0.293 AC: 1412 AN: 4820

European-Finnish (FIN) AF: 0.436 AC: 4601 AN: 10564

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33043 AN: 67970

Other (OTH) AF: 0.433 AC: 912 AN: 2108

Alfa AF: 0.289 Hom.: 749

Bravo AF: 0.381

Asia WGS AF: 0.206 AC: 721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.094
DANN	Benign	0.39
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs1245577; hg19: chr10-73810914;