rs11209979

Positions:

• chr1-72563930-T-A

Variant summary

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

The ENST00000665984.1(ENSG00000286863):​n.515+5944T>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 0.211 in 151,938 control chromosomes in the GnomAD database, including 3,628 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 0.21 (3628 hom., cov: 32)
• Consequence: ENST00000665984.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378797	XR_001737670.2	n.964+5944T>A		intron_variant, non_coding_transcript_variant
LOC105378797	XR_001737671.3	n.646+5944T>A		intron_variant, non_coding_transcript_variant
LOC105378797	XR_947505.3	n.834+5944T>A		intron_variant, non_coding_transcript_variant
LOC105378797	XR_947506.3	n.786+5944T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665984.1	n.515+5944T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32002 AN: 151820 Hom.: 3619 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.211 AC: 32040 AN: 151938 Hom.: 3628 Cov.: 32 AF XY: 0.202 AC XY: 15039 AN XY: 74288

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.0279

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.216

Alfa AF: 0.236 Hom.: 537

Bravo AF: 0.216

Asia WGS AF: 0.0890 AC: 307 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11209979; hg19: chr1-73029613;