rs6671426

chr1-2572795-C-Achr1-2572795-C-G

Variant summary

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

The NR_121638.1(LOC100996583):n.71+6190C>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 0.58 in 151,930 control chromosomes in the GnomAD database, including 27,210 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 0.58 (27210 hom., cov: 32)
• Consequence: LOC100996583 NR_121638.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

Genes affected

LOC100996583 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100996583	NR_121638.1	n.71+6190C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88070 AN: 151814 Hom.: 27161 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.580 AC: 88171 AN: 151930 Hom.: 27210 Cov.: 32 AF XY: 0.581 AC XY: 43156 AN XY: 74234

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.554

Alfa AF: 0.510 Hom.: 4172

Bravo AF: 0.586

Asia WGS AF: 0.678 AC: 2361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6671426; hg19: chr1-2504234;