rs7043482

Positions:

• chr9-82521000-A-C
• chr9-82521000-A-G
• chr9-82521000-A-T

Variant summary

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

The ENST00000637606.1(ENSG00000290551):​n.985+24142A>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 0.486 in 151,962 control chromosomes in the GnomAD database, including 21,156 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 0.49 (21156 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000637606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987087	XR_001746782.2	n.247+24142A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000637606.1	n.985+24142A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73717 AN: 151844 Hom.: 21086 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.486 AC: 73851 AN: 151962 Hom.: 21156 Cov.: 32 AF XY: 0.484 AC XY: 35951 AN XY: 74264

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.473

Alfa AF: 0.357 Hom.: 20531

Bravo AF: 0.509

Asia WGS AF: 0.552 AC: 1919 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
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: rs7043482; hg19: chr9-85135915; COSMIC: COSV73936731;