rs12617311

Positions:

• chr2-198767841-G-A

Variant summary

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

The ENST00000440609.1(ENSG00000225421):​n.98+4418C>T 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 0.283 in 151,784 control chromosomes in the GnomAD database, including 6,607 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 (6607 hom., cov: 30)
• Consequence: ENST00000440609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

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 (SAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373831	XR_923759.3	n.72+4418C>T		intron_variant, non_coding_transcript_variant
LOC105373831	XR_923760.2	n.72+4418C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000440609.1	n.98+4418C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42947 AN: 151666 Hom.: 6606 Cov.: 30

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.283 AC: 42973 AN: 151784 Hom.: 6607 Cov.: 30 AF XY: 0.285 AC XY: 21159 AN XY: 74150

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.301

Alfa AF: 0.323 Hom.: 12148

Bravo AF: 0.281

Asia WGS AF: 0.407 AC: 1417 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	12
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12617311; hg19: chr2-199632565;