rs11235464

Variant names:

• chr11-72199434-T-C
• rs11235464
• ENST00000378140.3:n.196-698A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000378140.3(ENSG00000204971):​n.196-698A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.01 in 152,128 control chromosomes in the GnomAD database, including 7 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 0.010 (7 hom., cov: 32)
• Consequence: ENSG00000204971 ENST00000378140.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 1 publications found

Genes affected

ENSG00000204971 (HGNC:58347):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.01 (1528/152128) while in subpopulation SAS AF = 0.0168 (81/4818). AF 95% confidence interval is 0.0151. There are 7 homozygotes in GnomAd4. There are 726 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 7 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000378140.3. 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
	FOLR1-AS1	NR_199595.1		n.196-698A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000204971	ENST00000378140.3	TSL:3	n.196-698A>G		intron	N/A
	ENSG00000204971	ENST00000824615.1		n.217+9613A>G		intron	N/A
	ENSG00000204971	ENST00000824616.1		n.290-698A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0101 AC: 1530 AN: 152012 Hom.: 7 Cov.: 32

Gnomad AFR AF: 0.00254

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00740

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.00843

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0159

Gnomad OTH AF: 0.00766

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

GnomAD4 genome AF: 0.0100 AC: 1528 AN: 152128 Hom.: 7 Cov.: 32 AF XY: 0.00976 AC XY: 726 AN XY: 74368

African (AFR) AF: 0.00253 AC: 105 AN: 41522

American (AMR) AF: 0.00740 AC: 113 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4818

European-Finnish (FIN) AF: 0.00843 AC: 89 AN: 10562

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0159 AC: 1082 AN: 67982

Other (OTH) AF: 0.00758 AC: 16 AN: 2112

Alfa AF: 0.0147 Hom.: 31

Bravo AF: 0.00931

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.73
DANN	Benign	0.19
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11235464;

hg19: chr11-71910478;