rs239627

chr21-27448105-T-Gchr21-27448105-T-Achr21-27448105-T-C

Variant summary

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

The ENST00000420186.2(ENSG00000231236):n.202+273A>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 0.842 in 152,060 control chromosomes in the GnomAD database, including 54,018 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 0.84 (54018 hom., cov: 30)
• Consequence: ENST00000420186.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

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 (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372762	XR_007067830.1	n.263+273A>C		intron_variant, non_coding_transcript_variant
LOC105372762	XR_001754990.2	n.263+273A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000420186.2	n.202+273A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127946 AN: 151942 Hom.: 53987 Cov.: 30

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.842 AC: 128036 AN: 152060 Hom.: 54018 Cov.: 30 AF XY: 0.843 AC XY: 62612 AN XY: 74310

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.816

Alfa AF: 0.843 Hom.: 4084

Bravo AF: 0.835

Asia WGS AF: 0.741 AC: 2577 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	1.8
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs239627; hg19: chr21-28820424;