rs1024034

Positions:

• chr4-11435538-A-G

Variant summary

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

The ENST00000662830.1(ENSG00000287778):​n.312+1123A>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 0.0758 in 152,262 control chromosomes in the GnomAD database, including 904 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 0.076 (904 hom., cov: 32)
• Consequence: ENST00000662830.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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
	ENST00000662830.1	n.312+1123A>G		intron_variant, non_coding_transcript_variant
	ENST00000656610.1	n.3723+1123A>G		intron_variant, non_coding_transcript_variant
	ENST00000670155.1	n.431+1123A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0757 AC: 11516 AN: 152144 Hom.: 900 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0774

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0758 AC: 11535 AN: 152262 Hom.: 904 Cov.: 32 AF XY: 0.0737 AC XY: 5486 AN XY: 74440

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.0487

Gnomad4 ASJ AF: 0.0774

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0323

Gnomad4 FIN AF: 0.0138

Gnomad4 NFE AF: 0.0294

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0476 Hom.: 167

Bravo AF: 0.0829

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024034; hg19: chr4-11437162;