rs1556413

Variant names:

• chr6-167111255-G-A
• rs1556413
• ENST00000705249.1:c.1066-24783G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-167111255-G-A
• chr6-167111255-G-C
• chr6-167111255-G-T

Variant summary

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

The ENST00000705249.1(ENSG00000272980):​c.1066-24783G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,054 control chromosomes in the GnomAD database, including 13,739 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 0.41 (13739 hom., cov: 32)
• Consequence: ENSG00000272980 ENST00000705249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

ENSG00000272980 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.504 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.1066-24783G>A		intron_variant	Intron 11 of 12			ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61955 AN: 151936 Hom.: 13729 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.408 AC: 62000 AN: 152054 Hom.: 13739 Cov.: 32 AF XY: 0.409 AC XY: 30428 AN XY: 74346

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.436

Alfa AF: 0.457 Hom.: 21354

Bravo AF: 0.406

Asia WGS AF: 0.421 AC: 1463 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	0.060
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1556413; hg19: chr6-167524743;