rs944141

chr9-5490522-C-T

Variant summary

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

The ENST00000661858.1(ENSG00000286162):n.277-31335G>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 0.264 in 152,098 control chromosomes in the GnomAD database, including 5,618 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 0.26 (5618 hom., cov: 32)
• Consequence: ENST00000661858.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902114	XR_007061406.1	n.256-31335G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661858.1	n.277-31335G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40083 AN: 151980 Hom.: 5609 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.264 AC: 40117 AN: 152098 Hom.: 5618 Cov.: 32 AF XY: 0.265 AC XY: 19728 AN XY: 74374

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.265

Alfa AF: 0.241 Hom.: 2350

Bravo AF: 0.274

Asia WGS AF: 0.279 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.28
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs944141; hg19: chr9-5490522;