rs263153

chr6-142628172-G-T

Variant summary

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

The NR_027312.1(LOC153910):n.177+9541C>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 0.0991 in 152,158 control chromosomes in the GnomAD database, including 851 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 0.099 (851 hom., cov: 32)
• Consequence: LOC153910 NR_027312.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC153910	NR_027312.1	n.177+9541C>A		intron_variant, non_coding_transcript_variant
LOC153910	NR_027311.1	n.124+9541C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000447311.1	n.177+9541C>A		intron_variant, non_coding_transcript_variant		2
	ENST00000635073.1	n.63+9541C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0991 AC: 15061 AN: 152040 Hom.: 852 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0673

Gnomad ASJ AF: 0.0929

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0279

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0920

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.0991 AC: 15072 AN: 152158 Hom.: 851 Cov.: 32 AF XY: 0.0994 AC XY: 7398 AN XY: 74390

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0672

Gnomad4 ASJ AF: 0.0929

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0281

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0920

Gnomad4 OTH AF: 0.0846

Alfa AF: 0.0903 Hom.: 337

Bravo AF: 0.0954

Asia WGS AF: 0.0270 AC: 95 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.053
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs263153; hg19: chr6-142949309;