1-209539544-T-C

Variant names:

• chr1-209539544-T-C
• rs6703183
• ENST00000424696.6:n.510+1154A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000424696.6(ENSG00000224260):​n.510+1154A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,074 control chromosomes in the GnomAD database, including 20,621 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 0.48 (20621 hom., cov: 33)
• Consequence: ENSG00000224260 ENST00000424696.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 14 publications found

Genes affected

ENSG00000224260 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424696.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224260	ENST00000424696.6	TSL:2	n.510+1154A>G		intron	N/A
	ENSG00000224260	ENST00000453331.1	TSL:3	n.502+1154A>G		intron	N/A
	ENSG00000224260	ENST00000782098.1		n.549+1154A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73053 AN: 151956 Hom.: 20562 Cov.: 33

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.481 AC: 73173 AN: 152074 Hom.: 20621 Cov.: 33 AF XY: 0.483 AC XY: 35921 AN XY: 74334

African (AFR) AF: 0.779 AC: 32308 AN: 41486

American (AMR) AF: 0.449 AC: 6856 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1430 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3267 AN: 5164

South Asian (SAS) AF: 0.384 AC: 1851 AN: 4820

European-Finnish (FIN) AF: 0.351 AC: 3706 AN: 10558

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22327 AN: 67980

Other (OTH) AF: 0.463 AC: 977 AN: 2112

Alfa AF: 0.385 Hom.: 44267

Bravo AF: 0.503

Asia WGS AF: 0.534 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs6703183; hg19: chr1-209712889;