6-98106018-G-A

Position:

• chr6-98106018-G-A

Variant summary

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

The ENST00000656098.1(ENSG00000271860):​n.1400+6748G>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 0.393 in 151,738 control chromosomes in the GnomAD database, including 12,728 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 0.39 (12728 hom., cov: 32)
• Consequence: ENST00000656098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656098.1	n.1400+6748G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59663 AN: 151620 Hom.: 12734 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.393 AC: 59649 AN: 151738 Hom.: 12728 Cov.: 32 AF XY: 0.391 AC XY: 28974 AN XY: 74136

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.393

Alfa AF: 0.426 Hom.: 1784

Bravo AF: 0.379

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1487441; hg19: chr6-98553894;