13-71318440-T-C

Variant names:

• chr13-71318440-T-C
• rs1005066

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 0.829 in 152,162 control chromosomes in the GnomAD database, including 52,438 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 0.83 (52438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.829 AC: 126085 AN: 152042 Hom.: 52410 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.829 AC: 126165 AN: 152162 Hom.: 52438 Cov.: 32 AF XY: 0.833 AC XY: 61964 AN XY: 74386

African (AFR) AF: 0.761 AC: 31560 AN: 41486

American (AMR) AF: 0.844 AC: 12901 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2907 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4597 AN: 5160

South Asian (SAS) AF: 0.831 AC: 4010 AN: 4826

European-Finnish (FIN) AF: 0.929 AC: 9863 AN: 10614

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57678 AN: 68008

Other (OTH) AF: 0.819 AC: 1730 AN: 2112

Alfa AF: 0.838 Hom.: 223723

Bravo AF: 0.818

Asia WGS AF: 0.848 AC: 2948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.48
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs1005066; hg19: chr13-71892572;