rs721357

Positions:

• chr2-223502061-A-C
• chr2-223502061-A-G
• chr2-223502061-A-T

Variant summary

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

The ENST00000422118.1(ENSG00000231189):​n.179-1921A>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 0.642 in 152,016 control chromosomes in the GnomAD database, including 31,617 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 0.64 (31617 hom., cov: 33)
• Consequence: ENST00000422118.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373907	XR_923952.4	n.182+2808A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000422118.1	n.179-1921A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97611 AN: 151898 Hom.: 31599 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.642 AC: 97668 AN: 152016 Hom.: 31617 Cov.: 33 AF XY: 0.639 AC XY: 47485 AN XY: 74268

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.614

Alfa AF: 0.651 Hom.: 52939

Bravo AF: 0.638

Asia WGS AF: 0.592 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs721357; hg19: chr2-224366779;