rs949911

Variant names:

• chr12-66019184-C-A
• rs949911
• ENST00000738605.1:n.93+1385G>T

Variant summary

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

The ENST00000738605.1(ENSG00000296369):​n.93+1385G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,148 control chromosomes in the GnomAD database, including 1,879 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 0.14 (1879 hom., cov: 32)
• Consequence: ENSG00000296369 ENST00000738605.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 2 publications found

Genes affected

ENSG00000296369 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296369	ENST00000738605.1	n.93+1385G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21118 AN: 152030 Hom.: 1876 Cov.: 32

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.139 AC: 21125 AN: 152148 Hom.: 1879 Cov.: 32 AF XY: 0.139 AC XY: 10329 AN XY: 74374

African (AFR) AF: 0.0326 AC: 1352 AN: 41530

American (AMR) AF: 0.168 AC: 2562 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 567 AN: 3464

East Asian (EAS) AF: 0.0340 AC: 176 AN: 5172

South Asian (SAS) AF: 0.142 AC: 684 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2122 AN: 10580

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13195 AN: 68000

Other (OTH) AF: 0.134 AC: 282 AN: 2104

Alfa AF: 0.178 Hom.: 3852

Bravo AF: 0.130

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	17
DANN	Benign	0.42
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs949911; hg19: chr12-66412964;