rs241404

Positions:

• chr6-32898220-T-C

Variant summary

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

The NR_037177.1(LOC100294145):​n.852-2700T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,984 control chromosomes in the GnomAD database, including 13,457 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 0.42 (13457 hom., cov: 31)
• Consequence: LOC100294145 NR_037177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260

Genes affected

ENSG00000289047 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100294145	NR_037177.1	n.852-2700T>C		intron_variant
LOC100294145	NR_037178.1	n.753-2700T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289047	ENST00000685247.2	n.714-2700T>C		intron_variant
ENSG00000289047	ENST00000701517.1	n.630-2700T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63262 AN: 151866 Hom.: 13458 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.416 AC: 63281 AN: 151984 Hom.: 13457 Cov.: 31 AF XY: 0.411 AC XY: 30544 AN XY: 74292

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.409

Alfa AF: 0.417 Hom.: 23283

Bravo AF: 0.415

Asia WGS AF: 0.372 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.1
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs241404; hg19: chr6-32865997;