rs12994941

Positions:

• chr2-41723586-T-C

Variant summary

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

The ENST00000660664.1(ENSG00000287145):​n.110-1101T>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 0.242 in 152,072 control chromosomes in the GnomAD database, including 4,537 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 0.24 (4537 hom., cov: 32)
• Consequence: ENST00000660664.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000660664.1	n.110-1101T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36804 AN: 151954 Hom.: 4538 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.242 AC: 36818 AN: 152072 Hom.: 4537 Cov.: 32 AF XY: 0.248 AC XY: 18449 AN XY: 74328

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.268

Alfa AF: 0.228 Hom.: 857

Bravo AF: 0.238

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12994941; hg19: chr2-41950726;