10-71859414-T-C

Variant names:

• chr10-71859414-T-C
• rs11597008

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 0.54 in 152,068 control chromosomes in the GnomAD database, including 24,513 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 0.54 (24513 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 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: 0.540 AC: 82063 AN: 151950 Hom.: 24509 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.540 AC: 82076 AN: 152068 Hom.: 24513 Cov.: 31 AF XY: 0.532 AC XY: 39523 AN XY: 74328

African (AFR) AF: 0.297 AC: 12317 AN: 41496

American (AMR) AF: 0.518 AC: 7908 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2333 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1641 AN: 5168

South Asian (SAS) AF: 0.555 AC: 2678 AN: 4824

European-Finnish (FIN) AF: 0.538 AC: 5683 AN: 10566

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47316 AN: 67968

Other (OTH) AF: 0.589 AC: 1245 AN: 2112

Alfa AF: 0.589 Hom.: 3766

Bravo AF: 0.523

Asia WGS AF: 0.444 AC: 1547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.65
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs11597008; hg19: chr10-73619171;