rs6575421

Positions:

• chr14-27085606-C-A
• chr14-27085606-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000656336.1(ENSG00000258081):​n.481-48364C>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 0.476 in 151,862 control chromosomes in the GnomAD database, including 17,547 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 0.48 (17547 hom., cov: 32)
• Consequence: ENST00000656336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.82

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370420	XR_943662.3	n.66-6395C>A		intron_variant, non_coding_transcript_variant
LOC105370420	XR_001750686.2	n.63+8306C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656336.1	n.481-48364C>A		intron_variant, non_coding_transcript_variant
	ENST00000552303.1	n.268+8306C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72299 AN: 151742 Hom.: 17536 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.476 AC: 72343 AN: 151862 Hom.: 17547 Cov.: 32 AF XY: 0.478 AC XY: 35484 AN XY: 74208

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.477

Alfa AF: 0.472 Hom.: 22960

Bravo AF: 0.474

Asia WGS AF: 0.382 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	18
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6575421; hg19: chr14-27554812;