rs11964461

Variant names:

• chr6-93520807-C-T
• rs11964461
• ENST00000668367.1:n.152-3846C>T

Variant summary

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

The ENST00000668367.1(ENSG00000287683):​n.152-3846C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 151,938 control chromosomes in the GnomAD database, including 73 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 0.020 (73 hom., cov: 32)
• Consequence: ENSG00000287683 ENST00000668367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 0 publications found

Genes affected

ENSG00000287683 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.059 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377899	XR_001744262.2	n.1389-3846C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287683	ENST00000668367.1	n.152-3846C>T		intron_variant	Intron 1 of 4
ENSG00000287683	ENST00000776530.1	n.170-3846C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0196 AC: 2970 AN: 151820 Hom.: 72 Cov.: 32

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00866

Gnomad ASJ AF: 0.00318

Gnomad EAS AF: 0.0234

Gnomad SAS AF: 0.00809

Gnomad FIN AF: 0.000190

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00138

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0196 AC: 2973 AN: 151938 Hom.: 73 Cov.: 32 AF XY: 0.0192 AC XY: 1426 AN XY: 74238

African (AFR) AF: 0.0610 AC: 2527 AN: 41458

American (AMR) AF: 0.00858 AC: 131 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.00318 AC: 11 AN: 3464

East Asian (EAS) AF: 0.0233 AC: 120 AN: 5160

South Asian (SAS) AF: 0.00810 AC: 39 AN: 4814

European-Finnish (FIN) AF: 0.000190 AC: 2 AN: 10540

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.00138 AC: 94 AN: 67924

Other (OTH) AF: 0.0157 AC: 33 AN: 2108

Alfa AF: 0.0138 Hom.: 10

Bravo AF: 0.0217

Asia WGS AF: 0.0140 AC: 47 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.96
DANN	Benign	0.26
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs11964461; hg19: chr6-94230525;