rs10195618

Positions:

• chr2-21259420-G-A
• chr2-21259420-G-C

Variant summary

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

The ENST00000435237.1(ENSG00000233005):​n.120+38126G>A 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 0.851 in 152,174 control chromosomes in the GnomAD database, including 55,519 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 0.85 (55519 hom., cov: 32)
• Consequence: ENST00000435237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

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 (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374317	XR_002959373.2	n.136-4278G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435237.1	n.120+38126G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000457901.1	n.111-4273G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000670105.1	n.256+521G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129483 AN: 152056 Hom.: 55511 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.851 AC: 129526 AN: 152174 Hom.: 55519 Cov.: 32 AF XY: 0.849 AC XY: 63143 AN XY: 74394

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.861

Alfa AF: 0.891 Hom.: 60931

Bravo AF: 0.847

Asia WGS AF: 0.912 AC: 3173 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	2.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10195618; hg19: chr2-21482292;