6-44730971-G-A

Position:

• chr6-44730971-G-A

Variant summary

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

The ENST00000671451.1(ENSG00000286417):​n.159+2892G>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 0.579 in 152,138 control chromosomes in the GnomAD database, including 25,746 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 0.58 (25746 hom., cov: 33)
• Consequence: ENST00000671451.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929770	XR_926855.3	n.144+2892G>A		intron_variant, non_coding_transcript_variant
LOC101929770	XR_007059598.1	n.144+2892G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000671451.1	n.159+2892G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.579 AC: 88011 AN: 152020 Hom.: 25710 Cov.: 33

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.579 AC: 88091 AN: 152138 Hom.: 25746 Cov.: 33 AF XY: 0.580 AC XY: 43131 AN XY: 74364

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.561

Alfa AF: 0.580 Hom.: 4325

Bravo AF: 0.583

Asia WGS AF: 0.415 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	14
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs227849; hg19: chr6-44698708;