rs2996127

Positions:

• chr6-58035886-A-G

Variant summary

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

The ENST00000641775.1(ENSG00000225096):​n.224-7549A>G 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 0.24 in 148,800 control chromosomes in the GnomAD database, including 4,892 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 0.24 (4892 hom., cov: 28)
• Consequence: ENST00000641775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901336	XR_007059628.1	n.31-2095T>C		intron_variant, non_coding_transcript_variant
LOC101927293	XR_001744180.1	n.3524-7549A>G		intron_variant, non_coding_transcript_variant
LOC101927293	XR_007059624.1	n.1041-7549A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641775.1	n.224-7549A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.240 AC: 35698 AN: 148686 Hom.: 4883 Cov.: 28

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.240 AC: 35735 AN: 148800 Hom.: 4892 Cov.: 28 AF XY: 0.232 AC XY: 16820 AN XY: 72622

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.0996

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.220

Alfa AF: 0.229 Hom.: 483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2996127; hg19: chr6-58362164;