rs1824965

Positions:

• chr4-56703381-T-C
• chr4-56703381-T-G

Variant summary

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

The ENST00000685954.1(ENSG00000288944):​n.307+190A>G 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 0.495 in 151,910 control chromosomes in the GnomAD database, including 19,056 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 0.50 (19056 hom., cov: 31)
• Consequence: ENST00000685954.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHAER1	XR_001741702.3	n.412+190A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000685954.1	n.307+190A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75249 AN: 151792 Hom.: 19054 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.495 AC: 75261 AN: 151910 Hom.: 19056 Cov.: 31 AF XY: 0.495 AC XY: 36740 AN XY: 74244

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.494

Alfa AF: 0.518 Hom.: 16325

Bravo AF: 0.486

Asia WGS AF: 0.386 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1824965; hg19: chr4-57569547;