rs11964472

Variant names:

• chr6-52328715-C-A
• rs11964472
• ENST00000729269.1:n.774-17266G>T

Variant summary

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

The ENST00000729269.1(ENSG00000295329):​n.774-17266G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,306 control chromosomes in the GnomAD database, including 1,316 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 0.13 (1316 hom., cov: 33)
• Consequence: ENSG00000295329 ENST00000729269.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 2 publications found

Genes affected

ENSG00000295329 (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 (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729269.1. 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
	ENSG00000295329	ENST00000729269.1		n.774-17266G>T		intron	N/A
	ENSG00000295345	ENST00000729407.1		n.103+16278C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19647 AN: 152188 Hom.: 1307 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.129 AC: 19662 AN: 152306 Hom.: 1316 Cov.: 33 AF XY: 0.128 AC XY: 9550 AN XY: 74478

African (AFR) AF: 0.126 AC: 5247 AN: 41548

American (AMR) AF: 0.101 AC: 1541 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 715 AN: 3468

East Asian (EAS) AF: 0.144 AC: 747 AN: 5192

South Asian (SAS) AF: 0.118 AC: 569 AN: 4824

European-Finnish (FIN) AF: 0.0848 AC: 900 AN: 10616

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9405 AN: 68034

Other (OTH) AF: 0.138 AC: 292 AN: 2110

Alfa AF: 0.139 Hom.: 6835

Bravo AF: 0.130

Asia WGS AF: 0.148 AC: 517 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	1.3
DANN	Benign	0.64
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs11964472; hg19: chr6-52193513;