rs11964561

Positions:

• chr6-8169567-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642149.1(ENSG00000232234):​n.206+22968G>A variant causes a intron, non coding transcript 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: ENST00000642149.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105374910	XR_001743950.2	n.187+1647G>A		intron_variant, non_coding_transcript_variant
LOC105374910	XR_926440.3	n.80+11307G>A		intron_variant, non_coding_transcript_variant
LOC105374910	XR_926441.3	n.187+1647G>A		intron_variant, non_coding_transcript_variant
LOC105374910	XR_926443.3	n.80+11307G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000642149.1	n.206+22968G>A		intron_variant, non_coding_transcript_variant
	ENST00000643749.1	n.142+66715G>A		intron_variant, non_coding_transcript_variant
	ENST00000644216.1	n.954+1647G>A		intron_variant, non_coding_transcript_variant
	ENST00000647315.1	n.179+22968G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0448

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.0350

Gnomad4 SAS AF: 0.0206

Gnomad4 FIN AF: 0.0205

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0697

Alfa AF: 0.0522 Hom.: 181

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11964561; hg19: chr6-8169800;