rs227854

Positions:

• chr6-44733298-A-G

Variant summary

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

The ENST00000671451.1(ENSG00000286417):​n.159+5219A>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 0.364 in 152,074 control chromosomes in the GnomAD database, including 11,097 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 0.36 (11097 hom., cov: 32)
• Consequence: ENST00000671451.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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 = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929770	XR_926855.3	n.144+5219A>G		intron_variant, non_coding_transcript_variant
LOC101929770	XR_007059596.1	n.251+1930A>G		intron_variant, non_coding_transcript_variant
LOC101929770	XR_007059597.1	n.251+1930A>G		intron_variant, non_coding_transcript_variant
LOC101929770	XR_007059598.1	n.144+5219A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000671451.1	n.159+5219A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55331 AN: 151956 Hom.: 11066 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.364 AC: 55396 AN: 152074 Hom.: 11097 Cov.: 32 AF XY: 0.365 AC XY: 27109 AN XY: 74310

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.352

Alfa AF: 0.339 Hom.: 1613

Bravo AF: 0.385

Asia WGS AF: 0.402 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.039
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs227854; hg19: chr6-44701035;