ENST00000435946.1:n.193+101421C>A

Variant names:

• chr6-74448550-C-A
• rs72960926
• ENST00000435946.1:n.193+101421C>A

Variant summary

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

The ENST00000435946.1(ENSG00000223786):​n.193+101421C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 152,100 control chromosomes in the GnomAD database, including 293 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 0.055 (293 hom., cov: 31)
• Consequence: ENSG00000223786 ENST00000435946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 6 publications found

Genes affected

ENSG00000223786 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.073 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435946.1. 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
	LOC101928516	NR_110856.1		n.193+101421C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223786	ENST00000435946.1	TSL:1	n.193+101421C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8409 AN: 151982 Hom.: 294 Cov.: 31

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0400

Gnomad EAS AF: 0.0784

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0553 AC: 8409 AN: 152100 Hom.: 293 Cov.: 31 AF XY: 0.0554 AC XY: 4115 AN XY: 74336

African (AFR) AF: 0.0144 AC: 597 AN: 41514

American (AMR) AF: 0.0570 AC: 870 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0400 AC: 139 AN: 3472

East Asian (EAS) AF: 0.0786 AC: 406 AN: 5166

South Asian (SAS) AF: 0.0715 AC: 344 AN: 4810

European-Finnish (FIN) AF: 0.0705 AC: 746 AN: 10576

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0747 AC: 5077 AN: 67986

Other (OTH) AF: 0.0450 AC: 95 AN: 2112

Alfa AF: 0.0640 Hom.: 108

Bravo AF: 0.0526

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.60
DANN	Benign	0.41
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs72960926; hg19: chr6-75158266;