rs10055544

Positions:

• chr5-92222904-G-A
• chr5-92222904-G-T

Variant summary

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

The ENST00000507217.5(ENSG00000250049):​n.304+18220G>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 0.0611 in 152,160 control chromosomes in the GnomAD database, including 289 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 0.061 (289 hom., cov: 32)
• Consequence: ENST00000507217.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.068 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
	ENST00000507217.5	n.304+18220G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000502934.1	n.172+18220G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0612 AC: 9298 AN: 152042 Hom.: 291 Cov.: 32

Gnomad AFR AF: 0.0481

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.00716

Gnomad SAS AF: 0.0716

Gnomad FIN AF: 0.0739

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0611 AC: 9295 AN: 152160 Hom.: 289 Cov.: 32 AF XY: 0.0606 AC XY: 4505 AN XY: 74396

Gnomad4 AFR AF: 0.0480

Gnomad4 AMR AF: 0.0522

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.00718

Gnomad4 SAS AF: 0.0712

Gnomad4 FIN AF: 0.0739

Gnomad4 NFE AF: 0.0697

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0632 Hom.: 361

Bravo AF: 0.0575

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10055544; hg19: chr5-91518721;