rs1844549

Positions:

• chr10-18714366-C-G

Variant summary

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

The ENST00000654305.1(ENSG00000234244):​n.93+4005C>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 0.171 in 151,968 control chromosomes in the GnomAD database, including 2,381 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 0.17 (2381 hom., cov: 32)
• Consequence: ENST00000654305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

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 (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376440	XR_930721.2	n.68+4005C>G		intron_variant, non_coding_transcript_variant
LOC105376440	XR_930720.2	n.51+4005C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654305.1	n.93+4005C>G		intron_variant, non_coding_transcript_variant
	ENST00000654415.1	n.78+4005C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25926 AN: 151850 Hom.: 2379 Cov.: 32

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.171 AC: 25937 AN: 151968 Hom.: 2381 Cov.: 32 AF XY: 0.170 AC XY: 12618 AN XY: 74298

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.164

Alfa AF: 0.193 Hom.: 375

Bravo AF: 0.165

Asia WGS AF: 0.175 AC: 607 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	1.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1844549; hg19: chr10-19003295;