rs4869987

Positions:

• chr6-151111235-A-C
• chr6-151111235-A-G
• chr6-151111235-A-T

Variant summary

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

The ENST00000415477.1(ENSG00000223598):​n.576-22855T>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 0.537 in 151,318 control chromosomes in the GnomAD database, including 22,159 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 0.54 (22159 hom., cov: 29)
• Consequence: ENST00000415477.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

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 (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901432	XR_007059813.1	n.342-22855T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000415477.1	n.576-22855T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81205 AN: 151204 Hom.: 22138 Cov.: 29

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.537 AC: 81269 AN: 151318 Hom.: 22159 Cov.: 29 AF XY: 0.533 AC XY: 39399 AN XY: 73908

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.536

Alfa AF: 0.519 Hom.: 3720

Bravo AF: 0.537

Asia WGS AF: 0.383 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4869987; hg19: chr6-151432371;