rs227855

Positions:

• chr6-44734615-T-C

Variant summary

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

The ENST00000671451.1(ENSG00000286417):​n.159+6536T>C 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 0.665 in 152,100 control chromosomes in the GnomAD database, including 34,719 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 0.66 (34719 hom., cov: 32)
• Consequence: ENST00000671451.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929770	XR_926855.3	n.144+6536T>C		intron_variant, non_coding_transcript_variant
LOC101929770	XR_007059596.1	n.251+3247T>C		intron_variant, non_coding_transcript_variant
LOC101929770	XR_007059597.1	n.251+3247T>C		intron_variant, non_coding_transcript_variant
LOC101929770	XR_007059598.1	n.144+6536T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000671451.1	n.159+6536T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100986 AN: 151982 Hom.: 34672 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.665 AC: 101081 AN: 152100 Hom.: 34719 Cov.: 32 AF XY: 0.664 AC XY: 49360 AN XY: 74348

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.643

Alfa AF: 0.633 Hom.: 3876

Bravo AF: 0.681

Asia WGS AF: 0.535 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs227855; hg19: chr6-44702352;