rs11048972

Variant names:

• chr12-27330924-A-G
• rs11048972
• ENST00000806970.1:n.249+1698T>C

Variant summary

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

The ENST00000806970.1(ENSG00000304890):​n.249+1698T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 152,248 control chromosomes in the GnomAD database, including 481 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 0.069 (481 hom., cov: 31)
• Consequence: ENSG00000304890 ENST00000806970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 4 publications found

Genes affected

ENSG00000304890 (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 (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902906	XR_007063255.1	n.176+1698T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304890	ENST00000806970.1	n.249+1698T>C		intron_variant	Intron 1 of 1
ENSG00000304890	ENST00000806971.1	n.233+1698T>C		intron_variant	Intron 1 of 2
ENSG00000304890	ENST00000806972.1	n.193+1698T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0695 AC: 10579 AN: 152130 Hom.: 481 Cov.: 31

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0445

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.0497

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0542

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

GnomAD4 genome AF: 0.0695 AC: 10576 AN: 152248 Hom.: 481 Cov.: 31 AF XY: 0.0686 AC XY: 5108 AN XY: 74432

African (AFR) AF: 0.0165 AC: 687 AN: 41554

American (AMR) AF: 0.0444 AC: 679 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5180

South Asian (SAS) AF: 0.0498 AC: 240 AN: 4824

European-Finnish (FIN) AF: 0.106 AC: 1121 AN: 10608

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7106 AN: 68012

Other (OTH) AF: 0.0541 AC: 114 AN: 2108

Alfa AF: 0.0962 Hom.: 111

Bravo AF: 0.0610

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.64
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs11048972; hg19: chr12-27483857;