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. The variant received -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
• Publications: 15 publications found

Genes affected

ENSG00000272980 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000705249.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272980	ENST00000705249.1		c.1066-24783G>A		intron	N/A	ENSP00000516101.1
	ENSG00000272980	ENST00000705250.1		c.844-24783G>A		intron	N/A	ENSP00000516102.1
	ENSG00000272980	ENST00000705254.1		c.673-24783G>A		intron	N/A	ENSP00000516106.1

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

African (AFR) AF: 0.219 AC: 9072 AN: 41480

American (AMR) AF: 0.513 AC: 7845 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1655 AN: 3472

East Asian (EAS) AF: 0.428 AC: 2207 AN: 5160

South Asian (SAS) AF: 0.421 AC: 2030 AN: 4820

European-Finnish (FIN) AF: 0.495 AC: 5225 AN: 10566

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32309 AN: 67964

Other (OTH) AF: 0.436 AC: 921 AN: 2110

Alfa AF: 0.452 Hom.: 26803

Bravo AF: 0.406

Asia WGS AF: 0.421 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.060
DANN	Benign	0.64
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1556413; hg19: chr6-167524743;