rs694739

Positions:

• chr11-64329761-A-G
• chr11-64329761-A-T

Variant summary

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

The ENST00000690790.2(ENSG00000236935):​n.256-2225T>C 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 0.28 in 152,182 control chromosomes in the GnomAD database, including 7,443 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 0.28 (7443 hom., cov: 33)
• Consequence: ENST00000690790.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723878	XR_428944.4	n.432-2225T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000690790.2	n.256-2225T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42586 AN: 152062 Hom.: 7441 Cov.: 33

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.280 AC: 42595 AN: 152182 Hom.: 7443 Cov.: 33 AF XY: 0.283 AC XY: 21066 AN XY: 74376

Gnomad4 AFR AF: 0.0715

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.264

Alfa AF: 0.354 Hom.: 14816

Bravo AF: 0.266

Asia WGS AF: 0.232 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.75
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs694739; hg19: chr11-64097233;