rs241403

Positions:

• chr6-32899215-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.852-1705T>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 0.525 in 151,972 control chromosomes in the GnomAD database, including 21,219 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 0.52 (21219 hom., cov: 32)
• Consequence: LOC100294145 NR_037177.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100294145	NR_037177.1	n.852-1705T>C		intron_variant, non_coding_transcript_variant
LOC100294145	NR_037178.1	n.753-1705T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701517.1	n.630-1705T>C		intron_variant, non_coding_transcript_variant
	ENST00000685247.2	n.714-1705T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79689 AN: 151854 Hom.: 21194 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.525 AC: 79764 AN: 151972 Hom.: 21219 Cov.: 32 AF XY: 0.524 AC XY: 38955 AN XY: 74286

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.509

Alfa AF: 0.512 Hom.: 4382

Bravo AF: 0.521

Asia WGS AF: 0.564 AC: 1961 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
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: rs241403; hg19: chr6-32866992;