rs11964561

Variant names:

• chr6-8169567-G-A
• rs11964561
• ENST00000642149.1:n.206+22968G>A

Variant summary

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

The ENST00000642149.1(ENSG00000232234):​n.206+22968G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0864 in 151,936 control chromosomes in the GnomAD database, including 1,158 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 0.086 (1158 hom., cov: 32)
• Consequence: ENSG00000232234 ENST00000642149.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 1 publications found

Genes affected

ENSG00000232234 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374910	XR_001743950.2	n.187+1647G>A		intron_variant	Intron 2 of 3
LOC105374910	XR_926440.3	n.80+11307G>A		intron_variant	Intron 1 of 3
LOC105374910	XR_926441.3	n.187+1647G>A		intron_variant	Intron 2 of 3
LOC105374910	XR_926443.3	n.80+11307G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232234	ENST00000642149.1	n.206+22968G>A		intron_variant	Intron 2 of 5
ENSG00000232234	ENST00000643749.1	n.142+66715G>A		intron_variant	Intron 1 of 4
ENSG00000232234	ENST00000644216.1	n.954+1647G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13091 AN: 151818 Hom.: 1151 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.0210

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0864 AC: 13127 AN: 151936 Hom.: 1158 Cov.: 32 AF XY: 0.0833 AC XY: 6186 AN XY: 74230

African (AFR) AF: 0.227 AC: 9370 AN: 41348

American (AMR) AF: 0.0448 AC: 685 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3468

East Asian (EAS) AF: 0.0350 AC: 181 AN: 5168

South Asian (SAS) AF: 0.0206 AC: 99 AN: 4812

European-Finnish (FIN) AF: 0.0205 AC: 217 AN: 10570

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0340 AC: 2312 AN: 67978

Other (OTH) AF: 0.0697 AC: 147 AN: 2108

Alfa AF: 0.0555 Hom.: 410

Bravo AF: 0.0938

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.6
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs11964561; hg19: chr6-8169800;