chr3-6053956-C-A

Variant names:

• chr3-6053956-C-A
• rs1949403
• ENST00000425894.2:n.1011-70020C>A

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.1011-70020C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,944 control chromosomes in the GnomAD database, including 36,210 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 0.68 (36210 hom., cov: 31)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351
• Publications: 1 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425894.2. 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
	ENSG00000229642	ENST00000425894.2	TSL:3	n.1011-70020C>A		intron	N/A
	ENSG00000229642	ENST00000779001.1		n.1158-70020C>A		intron	N/A
	ENSG00000229642	ENST00000779002.1		n.782-19301C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102836 AN: 151830 Hom.: 36183 Cov.: 31

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.677 AC: 102908 AN: 151944 Hom.: 36210 Cov.: 31 AF XY: 0.684 AC XY: 50785 AN XY: 74260

African (AFR) AF: 0.477 AC: 19731 AN: 41386

American (AMR) AF: 0.789 AC: 12028 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2678 AN: 3470

East Asian (EAS) AF: 0.880 AC: 4547 AN: 5166

South Asian (SAS) AF: 0.881 AC: 4252 AN: 4824

European-Finnish (FIN) AF: 0.713 AC: 7557 AN: 10596

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.733 AC: 49764 AN: 67934

Other (OTH) AF: 0.685 AC: 1447 AN: 2112

Alfa AF: 0.707 Hom.: 75392

Bravo AF: 0.672

Asia WGS AF: 0.851 AC: 2957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
DANN	Benign	0.77
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1949403; hg19: chr3-6095643;