2-8611333-A-G

Position:

• chr2-8611333-A-G

Variant summary

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

The ENST00000425678.1(ENSG00000231083):​n.174-3532T>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 0.533 in 152,218 control chromosomes in the GnomAD database, including 25,237 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 0.53 (25237 hom., cov: 33)
• Consequence: ENST00000425678.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373411	XR_001739274.1	n.107-3532T>C		intron_variant, non_coding_transcript_variant
LOC105373411	XR_007086198.1	n.217+1422T>C		intron_variant, non_coding_transcript_variant
LOC105373411	XR_922758.2	n.145-3532T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000425678.1	n.174-3532T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81183 AN: 152100 Hom.: 25225 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.533 AC: 81203 AN: 152218 Hom.: 25237 Cov.: 33 AF XY: 0.542 AC XY: 40316 AN XY: 74434

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.546

Alfa AF: 0.569 Hom.: 5866

Bravo AF: 0.514

Asia WGS AF: 0.799 AC: 2779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368928; hg19: chr2-8751463;