chr13-73348607-A-G

Variant names:

• chr13-73348607-A-G
• rs1411321

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 0.946 in 152,166 control chromosomes in the GnomAD database, including 68,440 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 0.95 (68440 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 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: 0.946 AC: 143842 AN: 152048 Hom.: 68393 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.946 AC: 143946 AN: 152166 Hom.: 68440 Cov.: 31 AF XY: 0.947 AC XY: 70415 AN XY: 74390

African (AFR) AF: 0.831 AC: 34457 AN: 41480

American (AMR) AF: 0.974 AC: 14890 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3379 AN: 3470

East Asian (EAS) AF: 0.980 AC: 5069 AN: 5174

South Asian (SAS) AF: 0.984 AC: 4746 AN: 4822

European-Finnish (FIN) AF: 0.996 AC: 10553 AN: 10592

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67630 AN: 68026

Other (OTH) AF: 0.959 AC: 2025 AN: 2112

Alfa AF: 0.968 Hom.: 25057

Bravo AF: 0.939

Asia WGS AF: 0.965 AC: 3356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0080
DANN	Benign	0.23
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs1411321; hg19: chr13-73922744;