rs730050

Positions:

• chr3-52314348-C-A
• chr3-52314348-C-G
• chr3-52314348-C-T

Variant summary

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

The XM_017006129.2(DNAH1):​c.-1812C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,094 control chromosomes in the GnomAD database, including 10,996 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 (10996 hom., cov: 32)
• Consequence: DNAH1 XM_017006129.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

DNAH1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH1	XM_017006129.2	c.-1812C>A		5_prime_UTR_variant	1/80		XP_016861618.1
DNAH1	XM_017006130.2	c.-1812C>A		5_prime_UTR_variant	1/79		XP_016861619.1
DNAH1	XM_017006131.2	c.-1812C>A		5_prime_UTR_variant	1/79		XP_016861620.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54349 AN: 151976 Hom.: 10990 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.357 AC: 54368 AN: 152094 Hom.: 10996 Cov.: 32 AF XY: 0.369 AC XY: 27409 AN XY: 74328

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.371

Alfa AF: 0.381 Hom.: 14565

Bravo AF: 0.347

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs730050; hg19: chr3-52348364;