rs73039162

Variant names:

• chr6-167092786-A-G
• rs73039162
• ENST00000705249.1:c.1066-43252A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000705249.1(ENSG00000272980):​c.1066-43252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,172 control chromosomes in the GnomAD database, including 1,190 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 0.10 (1190 hom., cov: 32)
• Consequence: ENSG00000272980 ENST00000705249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

Genes affected

ENSG00000272980 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 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
ENSG00000272980	ENST00000705249.1	c.1066-43252A>G		intron_variant	Intron 11 of 12			ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15455 AN: 152054 Hom.: 1184 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0881

Gnomad EAS AF: 0.0930

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.102 AC: 15490 AN: 152172 Hom.: 1190 Cov.: 32 AF XY: 0.103 AC XY: 7640 AN XY: 74404

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0602

Gnomad4 ASJ AF: 0.0881

Gnomad4 EAS AF: 0.0930

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.0513

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0713 Hom.: 131

Bravo AF: 0.104

Asia WGS AF: 0.131 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73039162; hg19: chr6-167506274;